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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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--- a/picard_CollectWgsMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_CollectWgsMetrics.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,11 +1,11 @@
-<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>compute metrics for evaluating of whole genome sequencing experiments</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="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>compute metrics for evaluating of whole genome sequencing experiments</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@
     ##set up input files
@@ -16,63 +16,56 @@
 
     picard
     CollectWgsMetrics
-    INPUT='$escaped_element_identifier'
-    OUTPUT="${outFile}"
-    REFERENCE_SEQUENCE="${reference_fasta_filename}"
-    MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
-    MINIMUM_BASE_QUALITY="${minimum_base_quality}"
-    COVERAGE_CAP="${coverage_cap}"
+    --INPUT '$escaped_element_identifier'
+    --OUTPUT '${outFile}'
+    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
+    --MINIMUM_MAPPING_QUALITY '${minimum_mapping_quality}'
+    --MINIMUM_BASE_QUALITY '${minimum_base_quality}'
+    --COVERAGE_CAP '${coverage_cap}'
 
-    VALIDATION_STRINGENCY="${validation_stringency}"
-    QUIET=true
-    VERBOSITY=ERROR
+    --VALIDATION_STRINGENCY '${validation_stringency}'
+    --QUIET true
+    --VERBOSITY ERROR
 
   ]]></command>
-  <inputs>
-    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
-    <conditional name="reference_source">
-      <param name="reference_source_selector" type="select" label="Load reference genome from">
-        <option value="cached">Local cache</option>
-        <option value="history">History</option>
-      </param>
-      <when value="cached">
-        <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
-          <options from_data_table="all_fasta">
+    <inputs>
+        <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Load reference genome from">
+                <option value="cached">Local cache</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">
+                    <options from_data_table="all_fasta">
           </options>
-          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-        </param>
-      </when>
-      <when value="history">
-        <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />
-      </when>
-    </conditional>
-    <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/>
-    <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/>
-    <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
-
-
-    <expand macro="VS" />
-
-  </inputs>
-
-  <outputs>
-    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="reference_source_selector" value="history" />
-      <param name="minimum_mapping_quality" value="20" />
-      <param name="minimum_base_quality" value="20" />
-      <param name="coverage_cap" value="250" />
-      <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" />
-      <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
-      <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
-    </test>
-  </tests>
-
-
-  <help>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference"/>
+            </when>
+        </conditional>
+        <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/>
+        <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/>
+        <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_source_selector" value="history"/>
+            <param name="minimum_mapping_quality" value="20"/>
+            <param name="minimum_base_quality" value="20"/>
+            <param name="coverage_cap" value="250"/>
+            <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa"/>
+            <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam"/>
+            <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -97,5 +90,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>