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Fixed output mixup
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Harrison Deng 2025-02-24 15:10:02 +00:00
parent c02b726745
commit dac4d5a620
1 changed files with 5 additions and 5 deletions
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10
autobigs-cli.xml
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@ -14,9 +14,9 @@
<command detect_errors="exit_code"><![CDATA[ <command detect_errors="exit_code"><![CDATA[
#if $mode.operation == "info": #if $mode.operation == "info":
#if $mode.select_info.retrieved == "schemes": #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 autoBIGS info --retrieve-bigsdb-schemas#for $scheme in $mode.select_info.schemes_list# '${scheme.selected_db}' #end for# --csv $info_schemes_out
#else if $mode.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_db_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" $stop_on_fail
@ -54,13 +54,13 @@
</inputs> </inputs>
<outputs> <outputs>
<data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv"> <data name="mlst_profiles_output" label="${tool.name} on ${on_string}" format="csv">
<filter>mode['operation'] == "st"</filter> <filter>mode['operation'] == 'st'</filter>
</data> </data>
<data name="info_db_out" label="${tool.name} supported Databases" format="csv"> <data name="info_db_out" label="${tool.name} supported Databases" format="csv">
<filter>mode['operation'] == "info" and mode['select_info']['retrieved'] == 'databases'</filter> <filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'databases'</filter>
</data> </data>
<data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv"> <data name="info_schemes_out" label="${tool.name} supported Schemes" format="csv">
<filter>mode['operation'] == "info" and mode['select_info']['retrieved'] == 'schemes'</filter> <filter>mode['operation'] == 'info' and mode['select_info']['retrieved'] == 'schemes'</filter>
</data> </data>
</outputs> </outputs>
<tests> <tests>