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

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

--- a/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,52 +1,45 @@
-<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>revert the original base qualities and add the mate cigar tag</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">1</token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>revert the original base qualities and add the mate cigar tag</description>
+    <macros>
+        <import>picard_macros.xml</import>
+        <token name="@WRAPPER_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
     @java_options@
-    picard
-    RevertOriginalBaseQualitiesAndAddMateCigar
+    picard RevertOriginalBaseQualitiesAndAddMateCigar
 
-    INPUT='$inputFile'
-    OUTPUT="${outFile}"
+    --INPUT '$inputFile'
+    --OUTPUT '${outFile}'
 
-    RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
-    MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}"
+    --RESTORE_ORIGINAL_QUALITIES '${restore_original_qualities}'
+    --MAX_RECORDS_TO_EXAMINE '${max_records_to_examine}'
 
-    SORT_ORDER=coordinate
-    VALIDATION_STRINGENCY="${validation_stringency}"
-    QUIET=true
-    VERBOSITY=ERROR
+    --SORT_ORDER coordinate
+    --VALIDATION_STRINGENCY '${validation_stringency}'
+    --QUIET true
+    --VERBOSITY ERROR
 
   ]]></command>
-  <inputs>
-    <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-    <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
-    <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>
-
-    <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
-      <param name="restore_original_qualities" value="True"/>
-      <param name="max_records_to_examine" value="10000"/>
-      <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
-    </test>
-  </tests>
-
-
-  <help>
+    <inputs>
+        <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+        <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
+        <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
+            <param name="restore_original_qualities" value="True"/>
+            <param name="max_records_to_examine" value="10000"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 **Purpose**
 
@@ -67,5 +60,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>