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

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

--- a/picard_FilterSamReads.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_FilterSamReads.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,88 +1,82 @@
-<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>include or exclude aligned and unaligned reads and read lists</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="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>include or exclude aligned and unaligned reads and read lists</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@
     ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
 
-    picard
-    SortSam
-    INPUT='$escaped_element_identifier'
-    OUTPUT=query_sorted_bam.bam
-    SORT_ORDER=queryname
-    VALIDATION_STRINGENCY=LENIENT
-    QUIET=true
-    VERBOSITY=ERROR
+    picard SortSam
+    --INPUT '$escaped_element_identifier'
+    --OUTPUT query_sorted_bam.bam
+    --SORT_ORDER queryname
+    --VALIDATION_STRINGENCY LENIENT
+    --QUIET true
+    --VERBOSITY ERROR
 
     &&
 
-    picard
-    FilterSamReads
-    INPUT=query_sorted_bam.bam
-    FILTER="${filter_type.filter}"
+    picard FilterSamReads
+    --INPUT query_sorted_bam.bam
+    --FILTER '${filter_type.filter}'
 
     #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
-      READ_LIST_FILE="${filter_type.read_list_file}"
+        --READ_LIST_FILE '${filter_type.read_list_file}'
     #end if
 
-    OUTPUT="${outFile}"
-    SORT_ORDER=coordinate
-    VALIDATION_STRINGENCY="${validation_stringency}"
-    QUIET=true
-    VERBOSITY=ERROR
+    --OUTPUT '${outFile}'
+    --SORT_ORDER coordinate
+    --VALIDATION_STRINGENCY '${validation_stringency}'
+    --QUIET true
+    --VERBOSITY ERROR
 
   ]]></command>
-  <inputs>
-    <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-    <conditional name="filter_type">
-      <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
-        <option value="includeAligned">Include aligned</option>
-        <option value="excludeAligned">Exclude aligned</option>
-        <option value="includeReadList">Include read list</option>
-        <option value="excludeReadList">Exclude read list</option>
-      </param>
-      <when value="includeAligned"/> <!-- do nothing -->
-      <when value="excludeAligned"/> <!-- do nothing -->
-      <when value="includeReadList">
-        <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/>
-      </when>
-      <when value="excludeReadList">
-        <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
-      </when>
-    </conditional>
-
-    <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
-      <param name="filter" value="includeReadList"/>
-      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
-      <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
-    </test>
-    <test>
-      <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
-      <param name="filter" value="excludeReadList"/>
-      <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
-      <param name="validation_stringency" value="LENIENT"/>
-      <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
-    </test>
-  </tests>
-
-
-  <help>
+    <inputs>
+        <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+        <conditional name="filter_type">
+            <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
+                <option value="includeAligned">Include aligned</option>
+                <option value="excludeAligned">Exclude aligned</option>
+                <option value="includeReadList">Include read list</option>
+                <option value="excludeReadList">Exclude read list</option>
+            </param>
+            <when value="includeAligned"/>
+            <!-- do nothing -->
+            <when value="excludeAligned"/>
+            <!-- do nothing -->
+            <when value="includeReadList">
+                <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/>
+            </when>
+            <when value="excludeReadList">
+                <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
+            </when>
+        </conditional>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
+            <param name="filter" value="includeReadList"/>
+            <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
+        </test>
+        <test>
+            <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
+            <param name="filter" value="excludeReadList"/>
+            <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
+            <param name="validation_stringency" value="LENIENT"/>
+            <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 **Purpose**
 
@@ -123,5 +117,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>