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

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
line wrap: on
line diff
--- a/picard_CollectAlignmentSummaryMetrics.xml	Mon Sep 25 08:32:17 2023 +0000
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Sun Mar 03 16:06:11 2024 +0000
@@ -1,11 +1,11 @@
-<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
-  <description>writes a file containing summary alignment metrics</description>
-  <macros>
-    <import>picard_macros.xml</import>
-    <token name="@WRAPPER_VERSION@">2</token>
-  </macros>
-  <expand macro="requirements" />
-  <command detect_errors="exit_code"><![CDATA[
+<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
+    <description>writes a file containing summary alignment metrics</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
@@ -14,79 +14,77 @@
 
     @handle_reference_source@
 
-    picard
-    CollectAlignmentSummaryMetrics
-    INPUT='$escaped_element_identifier'
-    OUTPUT="${outFile}"
-    MAX_INSERT_SIZE=${maxinsert}
+    picard CollectAlignmentSummaryMetrics
+    --INPUT '$escaped_element_identifier'
+    --OUTPUT '${outFile}'
+    --MAX_INSERT_SIZE ${maxinsert}
     #for $sequence in $adapters:
-        ADAPTER_SEQUENCE="${sequence.adapter}"
+        --ADAPTER_SEQUENCE '${sequence.adapter}'
     #end for
     #for $level in str($metric_accumulation_level).split(','):
-        METRIC_ACCUMULATION_LEVEL="${level}"
+        --METRIC_ACCUMULATION_LEVEL '${level}'
     #end for
-    IS_BISULFITE_SEQUENCED="${bisulphite}"
+    --IS_BISULFITE_SEQUENCED '${bisulphite}'
 
-    REFERENCE_SEQUENCE="${reference_fasta_filename}"
+    --REFERENCE_SEQUENCE '${reference_fasta_filename}'
 
-    ASSUME_SORTED="${assume_sorted}"
+    --ASSUME_SORTED '${assume_sorted}'
 
-    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"/>
+                    <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 following 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="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
+            <option value="ALL_READS" selected="True">All reads</option>
+            <option value="SAMPLE">Sample</option>
+            <option value="LIBRARY">Library</option>
+            <option value="READ_GROUP">Read group</option>
         </param>
-      </when>
-      <when value="history">
-        <param name="ref_file" type="data" format="fasta" label="Use the following 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="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL">
-      <option value="ALL_READS" selected="True">All reads</option>
-      <option value="SAMPLE">Sample</option>
-      <option value="LIBRARY">Library</option>
-      <option value="READ_GROUP">Read group</option>
-    </param>
-    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
-    <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
-    <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
-          <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
-    </repeat>
-    <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
-    <expand macro="VS" />
-
-  </inputs>
-  <outputs>
-    <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: tablular"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="bisulphite" value="false" />
-      <param name="assume_sorted" value="true" />
-      <repeat name="adapters">
-        <param name="adapter" value = ""/>
-      </repeat>
-      <param name="maxinsert" value="100000" />
-      <param name="reference_source_selector" value="history" />
-      <param name="ref_file" value="picard_CASM_ref.fa" />
-      <param name="inputFile" value="picard_CASM.bam" ftype="bam" />
-      <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
-    </test>
-  </tests>
-  <help>
+        <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
+        <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/>
+        <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences">
+            <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
+        </repeat>
+        <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
+        <expand macro="VS"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bisulphite" value="false"/>
+            <param name="assume_sorted" value="true"/>
+            <repeat name="adapters">
+                <param name="adapter" value=""/>
+            </repeat>
+            <param name="maxinsert" value="100000"/>
+            <param name="reference_source_selector" value="history"/>
+            <param name="ref_file" value="picard_CASM_ref.fa"/>
+            <param name="inputFile" value="picard_CASM.bam" ftype="bam"/>
+            <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -121,5 +119,5 @@
 @more_info@
 
   </help>
-  <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>