Mercurial > repos > iuc > tb_profiler_collate

diff tb_profiler_collate.xml @ 1:e9568d48ee11 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler commit 7dba70c70c9fe33353a0fd21803b11cfddc42c32
author iuc
date Tue, 21 Oct 2025 10:24:50 +0000
parents 9fae5576604a
children
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--- a/tb_profiler_collate.xml	Fri Sep 05 12:50:05 2025 +0000
+++ b/tb_profiler_collate.xml	Tue Oct 21 10:24:50 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="tb_profiler_collate" name="TB-Profiler Collate" version="@TOOL_VERSION@@VERSION_SUFFIX@" profile="21.05">
+<tool id="tb_profiler_collate" name="TB-Profiler Collate" version="@TOOL_VERSION@+galaxy1" profile="21.05">
   <description>Combines multiple TB-Profiler JSON reports into summary and variants reports</description>
 
   <macros>
@@ -17,15 +17,19 @@
     #end for
 
     tb-profiler collate --dir .
-
   ]]></command>
 
   <inputs>
     <param type="data_collection" name="input_files" label="TB-Profiler JSON Reports" collection_type="list" format="json" help="Enter a list of TB-Profiler JSON reports to collate."/>
   </inputs>
 
-  <outputs>
-    <data name="output_txt" format="txt" label="${tool.name} on ${on_string}: Summary Report" from_work_dir="tbprofiler.txt"/>
+  <outputs>  
+    <data name="output_tabular" format="tabular" label="${tool.name} on ${on_string}: Summary Report (tabular)" from_work_dir="tbprofiler.txt">
+        <actions>
+            <action name="column_names" type="metadata" default="sample,main_lineage,sub_lineage,spoligotype,drtype,target_median_depth,pct_reads_mapped,num_reads_mapped,num_dr_variants,num_other_variants,rifampicin,isoniazid,ethambutol,pyrazinamide,moxifloxacin,levofloxacin,bedaquiline,delamanid,pretomanid,linezolid,streptomycin,amikacin,kanamycin,capreomycin,clofazimine,ethionamide,para-aminosalicylic_acid,cycloserine"/>
+            <action type="metadata" name="detect_metadata"/>
+        </actions>
+    </data>
     <data name="output_csv" format="csv" label="${tool.name} on ${on_string}: Variants Report (CSV)" from_work_dir="tbprofiler.variants.csv"/>
     <data name="output_variants" format="txt" label="${tool.name} on ${on_string}: Variants Report (TXT)" from_work_dir="tbprofiler.variants.txt"/>
   </outputs>
@@ -38,7 +42,7 @@
               </collection>
           </param>
 
-          <output name="output_txt" file="tbprofiler_test_1_sample.txt"/>
+          <output name="output_tabular" file="tbprofiler_test_1_sample.txt" ftype="tabular"/>
           <output name="output_csv" file="tbprofiler_test_1_sample.variants.csv"/>
           <output name="output_variants" file="tbprofiler_test_1_sample.variants.txt"/>
       </test>