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

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

--- a/picard_AddCommentsToBam.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_AddCommentsToBam.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,49 +1,48 @@
-<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>add comments to BAM dataset</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="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>add comments to BAM dataset</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@
-    @symlink_element_identifier@
+    ## linking does not work, picard complains about not writable file. Hopefully this can be removed in future version.
+    ##@symlink_element_identifier@
+    #import re
+    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
+    cp '$inputFile' '$escaped_element_identifier' &&
+
     picard
       AddCommentsToBam
-      INPUT='$escaped_element_identifier'
-      OUTPUT="${outFile}"
+      --INPUT '$escaped_element_identifier'
+      --OUTPUT '${outFile}'
       #for $element in $comments:
-        COMMENT="${element.comment}"
+          --COMMENT '${element.comment}'
       #end for
-      QUIET=true
-      VERBOSITY=ERROR
-      VALIDATION_STRINGENCY=${validation_stringency}
+      --QUIET true
+      --VERBOSITY ERROR
+      --VALIDATION_STRINGENCY ${validation_stringency}
   ]]></command>
-
-  <inputs>
-    <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
-    <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
-          <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
-    </repeat>
-
-    <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
-  </outputs>
-
-
-  <tests>
-  <test>
-      <param name="inputFile" value="picard_AddCommentsToBam.bam" />
-      <param name="comment" value="test1" />
-      <param name="validation_stringency" value="LENIENT" />
-      <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
-    </test>
-  </tests>
-  <help>
+    <inputs>
+        <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+        <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
+            <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
+        </repeat>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_AddCommentsToBam.bam"/>
+            <param name="comment" value="test1"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -60,5 +59,5 @@
 
 @more_info@
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>