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Jenkinsfile
vendored
16
Jenkinsfile
vendored
@ -2,29 +2,27 @@ pipeline {
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agent {
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agent {
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kubernetes {
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kubernetes {
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cloud 'rsys-devel'
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cloud 'rsys-devel'
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defaultContainer 'miniforge3'
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defaultContainer 'pip'
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inheritFrom 'miniforge'
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inheritFrom 'pip'
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}
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}
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}
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}
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stages {
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stages {
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stage ("install") {
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stage ("install") {
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steps {
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steps {
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sh 'conda env update -n base --file environment.yml'
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sh 'pip install -r requirements.txt'
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sh 'useradd galaxy -m'
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sh 'planemo ci_setup'
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sh 'apt-get update'
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sh 'apt-get install sudo -y'
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}
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}
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}
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}
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stage ("lint") {
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stage ("lint") {
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steps {
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steps {
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sh "sudo -u galaxy planemo lint autobigs-cli.xml"
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sh "planemo lint autobigs-cli.xml"
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}
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}
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}
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}
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stage ("test") {
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stage ("test") {
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steps {
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steps {
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sh 'sudo -u galaxy mkdir test_results'
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sh 'mkdir test_results'
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sh "sudo -u galaxy planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html"
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sh "planemo test autobigs-cli.xml --test_output_junit test_results/junit_results.xml --test_output_json test_results/results.json --test_output test_results/human.html"
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xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)]
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xunit checksName: '', tools: [JUnit(excludesPattern: '', pattern: 'test_results/junit_report.xml', stopProcessingIfError: true)]
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}
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}
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}
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}
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162
autobigs-cli.xml
162
autobigs-cli.xml
@ -1,76 +1,76 @@
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<tool id="autobigs-cli" name="autoBIGS.cli" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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<tool id="autobigs-cli" name="autoBIGS.cli" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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<description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
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<description>Automated MLST typing from PubMLST and InstitutPasteur.</description>
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<macros>
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<macros>
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<token name="@TOOL_VERSION@">0.5.0</token>
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<token name="@TOOL_VERSION@">0.5.0</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<import>autobigs-cli_macros.xml</import>
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<import>autobigs-cli_macros.xml</import>
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<expand macro="bio_tools"/>
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<expand macro="bio_tools"/>
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</macros>
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</macros>
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<requirements>
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">autobigs-cli</requirement>
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<requirement type="package" version="@TOOL_VERSION@">autobigs-cli</requirement>
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</requirements>
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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<command detect_errors="exit_code"><![CDATA[
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#if $mode.operation == "info":
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#if $mode.operation == "info":
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#if $mode.select_info.retrieved == "schemes":
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#if $mode.select_info.retrieved == "schemes":
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autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_schemes_out
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autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_schemes_out
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#else if $mode.select_info.retrieved == "databases":
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#else if $mode.select_info.retrieved == "databases":
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autoBIGS info --retrieve-bigsdbs --csv $info_db_out
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autoBIGS info --retrieve-bigsdbs --csv $info_db_out
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#end if
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#end if
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#else if $mode.operation == "st":
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#else if $mode.operation == "st":
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autoBIGS st#for $fasta in $mode.fastas_list# '${fasta.fasta}' #end for#"$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
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autoBIGS st#for $fasta in $mode.fastas_list# '${fasta.fasta}' #end for#"$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
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#end if
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#end if
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]]></command>
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]]></command>
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<inputs>
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<inputs>
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<conditional name="mode">
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<conditional name="mode">
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<param name="operation" label="Operation" type="select">
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<param name="operation" label="Operation" type="select">
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<option value="info">Retrieve Database Information</option>
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<option value="info">Retrieve Database Information</option>
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<option value="st">Perform Sequence Typing</option>
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<option value="st">Perform Sequence Typing</option>
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</param>
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</param>
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<when value="info">
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<when value="info">
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<conditional name="select_info">
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<conditional name="select_info">
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<param name="retrieved" label="Schemes or Database List" type="select">
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<param name="retrieved" label="Schemes or Database List" type="select">
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<option value="schemes">Available Schemas for Database</option>
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<option value="schemes">Available Schemas for Database</option>
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<option value="databases">Available Databases</option>
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<option value="databases">Available Databases</option>
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</param>
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</param>
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<when value="schemes">
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<when value="schemes">
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<repeat name="schemes_list" title="Schemes" min="1">
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<repeat name="schemes_list" title="Schemes" min="1">
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<param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
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<param name="selected_db" argument="--retrieve-bigsdb-schemas" label="Database to retrieve schemes from" type="text"/>
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</repeat>
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</repeat>
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</when>
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</when>
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<when value="databases">
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<when value="databases">
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</when>
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</when>
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</conditional>
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</conditional>
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</when>
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</when>
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<when value="st">
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<when value="st">
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<repeat name="fastas_list" title="Fasta" min="1">
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<repeat name="fastas_list" title="Fasta" min="1">
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<param name="fasta" label="FASTA file" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
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<param name="fasta" label="FASTA file" type="data" format="fasta,fas,fa,fna,ffn,faa,mpfa,frn"/>
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</repeat>
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</repeat>
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<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
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<param name="seqdefdb" label="BIGSdb SeqDef Name" type="text" optional="false"/>
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<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
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<param name="schema" label="BIGSdb SeqDef Schema ID" type="integer" min="0"/>
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<param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
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<param name="stop_on_fail" label="Stop on failure to match" truevalue="--sof" falsevalue="" value="false" type="boolean"/>
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</when>
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</when>
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</conditional>
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</conditional>
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</inputs>
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</inputs>
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<outputs>
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<outputs>
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<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
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<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
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<filter>mode['operation'] == 'st'</filter>
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<filter>mode['operation'] == 'st'</filter>
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</data>
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</data>
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<data name="info_db_out" label="${tool.name} supported Databases" format="csv">
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<data name="info_db_out" label="${tool.name} supported Databases" format="csv">
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<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'databases'</filter>
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<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'databases'</filter>
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</data>
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</data>
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<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
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<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
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<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'schemes'</filter>
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<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'schemes'</filter>
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</data>
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</data>
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</outputs>
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</outputs>
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<tests>
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<tests>
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<test expect_num_outputs="1">
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<test expect_num_outputs="1">
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<param name="operation" value="st" />
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<param name="operation" value="st" />
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<repeat name="fastas_list">
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<repeat name="fastas_list">
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<param name="fasta" value="tohama_I_minimized_features.fasta" />
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<param name="fasta" value="tohama_I_minimized_features.fasta" />
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</repeat>
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</repeat>
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<param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
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<param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
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<param name="schema" value="3" />
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<param name="schema" value="3" />
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<output name="mlst_profiles_output" file="tohama_I_minimized_features_typed.csv" ftype="csv" />
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<output name="mlst_profiles_output" file="tohama_I_minimized_features_typed.csv" ftype="csv" />
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@ -79,26 +79,26 @@
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<param name="operation" value="info" />
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<param name="operation" value="info" />
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<param name="retrieved" value="databases" />
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<param name="retrieved" value="databases" />
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<output name="info_db_out">
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<output name="info_db_out">
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<assert_contents>
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<assert_contents>
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<has_text text="BIGSdb Names,Source"/>
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<has_text text="BIGSdb Names,Source"/>
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<has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
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<has_text text="pubmlst_bordetella_seqdef,https://bigsdb.pasteur.fr/api"/>
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</assert_contents>
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</assert_contents>
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</output>
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</output>
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</test>
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</test>
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<test expect_num_outputs="1">
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<test expect_num_outputs="1">
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<param name="operation" value="info" />
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<param name="operation" value="info" />
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<repeat name="schemes_list">
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<repeat name="schemes_list">
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<param name="selected_db" value="pubmlst_bordetella_seqdef" />
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<param name="selected_db" value="pubmlst_bordetella_seqdef" />
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</repeat>
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</repeat>
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<output name="info_schemes_out">
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<output name="info_schemes_out">
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<assert_contents>
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<assert_contents>
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<has_text text="Name,ID"/>
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<has_text text="Name,ID"/>
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<has_text text="MLST,3"/>
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<has_text text="MLST,3"/>
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</assert_contents>
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</assert_contents>
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</output>
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</output>
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</test>
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</test>
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</tests>
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</tests>
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<help><![CDATA[
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<help><![CDATA[
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usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]] [--csv CSV_OUTPUT]
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usage: autoBIGS info [-h] [--retrieve-bigsdbs] [--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS [LIST_BIGSDB_SCHEMAS ...]] [--csv CSV_OUTPUT]
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@ -125,7 +125,7 @@ positional arguments:
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options:
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options:
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-h, --help show this help message and exit
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-h, --help show this help message and exit
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--stop-on-fail, -sof Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches).
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--stop-on-fail, -sof Should the algorithm stop in the case there are no matches (or partial matches when expecting exact matches).
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]]></help>
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]]></help>
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<citations>
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<citations>
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<citation type="bibtex">
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<citation type="bibtex">
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@book{Deng2025RealYHD,
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@book{Deng2025RealYHD,
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