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Attempting to add 3rd test for scheme retrieval
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Harrison Deng
2025-02-24 14:19:23 +00:00
parent d2dfbb9464
commit c02b726745
1 changed files with 20 additions and 8 deletions
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28
autobigs-cli.xml
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@@ -12,13 +12,13 @@
</requirements>
<command detect_errors="exit_code"><![CDATA[
#if $mode['operation'] == "info":
#if $select_info['retrieved'] == "schemas":
autoBIGS info $selected_schema --csv $info_db_out
#else if $select_info['retrieved'] == "databases":
#if $mode.operation == "info":
#if $mode.select_info.retrieved == "schemes":
autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_db_out
#else if $mode.select_info.retrieved == "databases":
autoBIGS info --retrieve-bigsdbs --csv $info_schemes_out
#end if
#else if $mode['operation'] == "st":
#else if $mode.operation == "st":
autoBIGS st "$fastas" "$seqdefdb" $schema "$mlst_profiles_output" $stop_on_fail
#end if
]]></command>
@@ -30,7 +30,7 @@
</param>
<when value="info">
<conditional name="select_info">
<param name="retrieved" label="Schemas or Database List" type="select">
<param name="retrieved" label="Schemes or Database List" type="select">
<option value="schemes">Available Schemas for Database</option>
<option value="databases">Available Databases</option>
</param>
@@ -57,10 +57,10 @@
<filter>mode['operation'] == "st"</filter>
</data>
<data name="info_db_out" label="${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 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>
</outputs>
<tests>
@@ -81,6 +81,18 @@
</assert_contents>
</output>
</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>
<help><![CDATA[