Harrison Deng
ddb98514fb
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143 lines
6.6 KiB
XML
143 lines
6.6 KiB
XML
<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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<macros>
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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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<import>autobigs-cli_macros.xml</import>
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<expand macro="bio_tools"/>
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</macros>
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">autobigs-cli</requirement>
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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#if $mode.operation == "info":
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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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#else if $mode.select_info.retrieved == "databases":
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autoBIGS info --retrieve-bigsdbs --csv $info_db_out
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#end if
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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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#end if
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]]></command>
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<inputs>
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<conditional name="mode">
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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="st">Perform Sequence Typing</option>
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</param>
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<when value="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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<option value="schemes">Available Schemas for Database</option>
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<option value="databases">Available Databases</option>
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</param>
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<when value="schemes">
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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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</repeat>
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</when>
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<when value="databases">
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</when>
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</conditional>
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</when>
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<when value="st">
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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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</repeat>
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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="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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</conditional>
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</inputs>
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<outputs>
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<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
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<filter>mode['operation'] == 'st'</filter>
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</data>
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<data name="info_db_out" label="${tool.name} supported Databases" format="csv">
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<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'databases'</filter>
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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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<filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'schemes'</filter>
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</data>
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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<param name="operation" value="st" />
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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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</repeat>
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<param name="seqdefdb" value="pubmlst_bordetella_seqdef" />
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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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</test>
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<test expect_num_outputs="1">
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<param name="operation" value="info" />
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<param name="retrieved" value="databases" />
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<output name="info_db_out">
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<assert_contents>
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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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</assert_contents>
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</output>
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</test>
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<test expect_num_outputs="1">
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<param name="operation" value="info" />
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<repeat name="schemes_list">
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<param name="selected_db" value="pubmlst_bordetella_seqdef" />
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</repeat>
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<output name="info_schemes_out">
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<assert_contents>
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<has_text text="Name,ID"/>
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<has_text text="MLST,3"/>
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</assert_contents>
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</output>
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</test>
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</tests>
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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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Fetches the latest BIGSdb MLST database definitions.
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options:
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-h, --help show this help message and exit
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--retrieve-bigsdbs, -l
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Lists all known BIGSdb MLST databases (fetched from known APIs and cached).
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--retrieve-bigsdb-schemas LIST_BIGSDB_SCHEMAS
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Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given.
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--csv, -o CSV_OUTPUT Output list as CSV at a given path. A suffix is added depending on the action taken.
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usage: autoBIGS st [-h] [--stop-on-fail] fastas [fastas ...] seqdefdb schema out
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Returns MLST exact profile matches.
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positional arguments:
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fastas The FASTA files to process. Multiple can be listed.
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seqdefdb The BIGSdb seqdef database to use for typing.
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schema The BIGSdb seqdef database schema ID (integer) to use for typing.
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out The output CSV name (.csv will be appended).
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options:
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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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]]></help>
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<citations>
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<citation type="bibtex">
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@book{Deng2025RealYHD,
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title = {Syph-and-VPD-Lab/autoBIGS.cli},
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url = {https://github.com/Syph-and-VPD-Lab/autoBIGS.cli},
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author = {Deng, Harrison},
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date = {2025-01-24},
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year = {2025},
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month = {1},
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day = {24},
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}
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</citation>
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</citations>
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</tool>
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