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comparison picard_CollectWgsMetrics.xml @ 12:05087b27692a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:50 -0500
parents 3a3234d7a2e8
children 7e6fd3d0f16e
comparison
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
2 <description>compute metrics for evaluating of whole genome sequencing experiments</description> 2 <description>compute metrics for evaluating of whole genome sequencing experiments</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 ##set up input files 9 ##set up input files
10 10
11 #set $reference_fasta_filename = "localref.fa" 11 #set $reference_fasta_filename = "localref.fa"
12 12
13 #if str( $reference_source.reference_source_selector ) == "history": 13 #if str( $reference_source.reference_source_selector ) == "history":
14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
15 #else: 15 #else:
16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
17 #end if 17 #end if
18 18
19 java -jar \$JAVA_JAR_PATH/picard.jar 19 picard
20 CollectWgsMetrics 20 CollectWgsMetrics
21 INPUT="${inputFile}" 21 INPUT="${inputFile}"
22 OUTPUT="${outFile}" 22 OUTPUT="${outFile}"
23 REFERENCE_SEQUENCE="${reference_fasta_filename}" 23 REFERENCE_SEQUENCE="${reference_fasta_filename}"
24 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" 24 MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}"
27 27
28 VALIDATION_STRINGENCY="${validation_stringency}" 28 VALIDATION_STRINGENCY="${validation_stringency}"
29 QUIET=true 29 QUIET=true
30 VERBOSITY=ERROR 30 VERBOSITY=ERROR
31 31
32 </command> 32 ]]></command>
33 <inputs> 33 <inputs>
34 <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"/> 34 <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"/>
35 <conditional name="reference_source"> 35 <conditional name="reference_source">
36 <param name="reference_source_selector" type="select" label="Load reference genome from"> 36 <param name="reference_source_selector" type="select" label="Load reference genome from">
37 <option value="cached">Local cache</option> 37 <option value="cached">Local cache</option>
71 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> 71 <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" />
72 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 72 <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
73 </test> 73 </test>
74 </tests> 74 </tests>
75 75
76 <stdio>
77 <exit_code range="1:" level="fatal"/>
78 </stdio>
79 76
80 <help> 77 <help>
81 78
82 .. class:: infomark 79 .. class:: infomark
83 80