ydeng/autoBIGS.galaxy
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Attempting to add 3rd test for scheme retrieval
Some checks reported errors
autoBIGS.galaxy/pipeline/head Something is wrong with the build of this commit
Details

Browse Source
This commit is contained in:
Harrison Deng 2025-02-24 14:19:23 +00:00
parent d2dfbb9464
commit c02b726745
1 changed files with 20 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

28
autobigs-cli.xml
View File

@ -12,13 +12,13 @@
</requirements> </requirements>
<command detect_errors="exit_code"><![CDATA[ <command detect_errors="exit_code"><![CDATA[
#if $mode['operation'] == "info": #if $mode.operation == "info":
#if $select_info['retrieved'] == "schemas": #if $mode.select_info.retrieved == "schemes":
autoBIGS info $selected_schema --csv $info_db_out autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_db_out
#else if $select_info['retrieved'] == "databases": #else if $mode.select_info.retrieved == "databases":
autoBIGS info --retrieve-bigsdbs --csv $info_schemes_out autoBIGS info --retrieve-bigsdbs --csv $info_schemes_out
#end if #end if
#else if $mode['operation'] == "st": #else if $mode.operation == "st":
autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
#end if #end if
]]></command> ]]></command>
@ -30,7 +30,7 @@
</param> </param>
<when value="info"> <when value="info">
<conditional name="select_info"> <conditional name="select_info">
<param name="retrieved" label="Schemas or Database List" type="select"> <param name="retrieved" label="Schemes or Database List" type="select">
<option value="schemes">Available Schemas for Database</option> <option value="schemes">Available Schemas for Database</option>
<option value="databases">Available Databases</option> <option value="databases">Available Databases</option>
</param> </param>
@ -57,10 +57,10 @@
<filter>mode['operation'] == "st"</filter> <filter>mode['operation'] == "st"</filter>
</data> </data>
<data name="info_db_out" label="${tool.name} supported Databases" format="csv"> <data name="info_db_out" label="${tool.name} supported Databases" format="csv">
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'databases'</filter> <filter>mode['operation'] == "info" and mode['select_info']['retrieved'] == 'databases'</filter>
</data> </data>
<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv"> <data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
<filter>mode['operation'] == "info" and select_info['retrieved'] == 'schemes'</filter> <filter>mode['operation'] == "info" and mode['select_info']['retrieved'] == 'schemes'</filter>
</data> </data>
</outputs> </outputs>
<tests> <tests>
@ -81,6 +81,18 @@
</assert_contents> </assert_contents>
</output> </output>
</test> </test>
<test expect_num_outputs="1">
<param name="operation" value="info" />
<repeat name="schemes_list">
<param name="selected_db" value="pubmlst_bordetella_seqdef" />
</repeat>
<output name="info_schemes_out">
<assert_contents>
<has_text text="Name,ID"/>
<has_text text="MLST,3"/>
</assert_contents>
</output>
</test>
</tests> </tests>
<help><![CDATA[ <help><![CDATA[