diff picard_AddOrReplaceReadGroups.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

--- a/picard_AddOrReplaceReadGroups.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_AddOrReplaceReadGroups.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,59 +1,53 @@
-<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>add or replaces read group information</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <import>read_group_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>add or replaces read group information</description>
+    <macros>
+        <import>picard_macros.xml</import>
+        <import>read_group_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
     @define_read_group_helpers@
     #set $rg_auto_name = $read_group_name_default($inputFile)
     @set_read_group_vars@
     @java_options@
     @symlink_element_identifier@
-    picard
-      AddOrReplaceReadGroups
-      INPUT='$escaped_element_identifier'
-      $format_read_group("RGLB=", $rg_lb, '"')
-      $format_read_group("RGPL=", $rg_pl, '"')
-      $format_read_group("RGPU=", $rg_pu, '"')
-      $format_read_group("RGSM=", $rg_sm, '"')
-      $format_read_group("RGID=", $rg_id, '"')
-      $format_read_group("RGDS=", $rg_ds, '"')
-      $format_read_group("RGPI=", $rg_pi, '"')
-      $format_read_group("RGDT=", $rg_dt, '"')
-      VALIDATION_STRINGENCY="${validation_stringency}"
-      QUIET=true
-      VERBOSITY=ERROR
-      OUTPUT="${outFile}"
+    picard AddOrReplaceReadGroups
+      --INPUT '$escaped_element_identifier'
+      $format_read_group("", $rg_lb, quote='"', arg=" --RGLB ")
+      $format_read_group("", $rg_pl, quote='"', arg=" --RGPL ")
+      $format_read_group("", $rg_pu, quote='"', arg=" --RGPU ")
+      $format_read_group("", $rg_sm, quote='"', arg=" --RGSM ")
+      $format_read_group("", $rg_id, quote='"', arg=" --RGID ")
+      $format_read_group("", $rg_ds, quote='"', arg=" --RGDS ")
+      $format_read_group("", $rg_pi, quote='"', arg=" --RGPI ")
+      $format_read_group("", $rg_dt, quote='"', arg=" --RGDT ")
+      --OUTPUT '${outFile}'
+      --VALIDATION_STRINGENCY '${validation_stringency}'
+      --QUIET true
+      --VERBOSITY ERROR
 
   ]]></command>
-
-  <inputs>
-    <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
-    <expand macro="read_group_inputs_picard" />
-    <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
-  </outputs>
-
-
-  <tests>
-    <test>
-      <param name="inputFile" value="picard_ARRG.bam" />
-      <param name="LB" value="tumor-a" />
-      <param name="PL" value="ILLUMINA" />
-      <param name="PU" value="run-1" />
-      <param name="SM" value="sample-a" />
-      <param name="ID" value="id-1" />
-      <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam" />
-    </test>
-  </tests>
-  <help>
+    <inputs>
+        <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+        <expand macro="read_group_inputs_picard"/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_ARRG.bam"/>
+            <param name="LB" value="tumor-a"/>
+            <param name="PL" value="ILLUMINA"/>
+            <param name="PU" value="run-1"/>
+            <param name="SM" value="sample-a"/>
+            <param name="ID" value="id-1"/>
+            <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -107,5 +101,5 @@
 
 @more_info@
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>