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comparison picard_CollectInsertSizeMetrics.xml @ 7:08f69add4d06 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 15:11:36 -0500
parents 52fdfc45590a
children e417b1d6288d
comparison
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
2 <description>plots distribution of insert sizes</description> 2 <description>plots distribution of insert sizes</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 <requirement type="package" version="3.1.2">R</requirement> 7 <requirement type="package" version="3.3.1">r</requirement>
8 </expand> 8 </expand>
9 <command> 9 <command detect_errors="exit_code"><![CDATA[
10 @java_options@ 10 @java_options@
11 ##set up input files 11 ##set up input files
12 12
13 #set $reference_fasta_filename = "localref.fa" 13 #set $reference_fasta_filename = "localref.fa"
14 14
15 #if str( $reference_source.reference_source_selector ) == "history": 15 #if str( $reference_source.reference_source_selector ) == "history":
16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 16 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
17 #else: 17 #else:
18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 18 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
19 #end if 19 #end if
20 20
21 java -jar \$JAVA_JAR_PATH/picard.jar 21 picard
22 CollectInsertSizeMetrics 22 CollectInsertSizeMetrics
23 INPUT="${inputFile}" 23 INPUT="${inputFile}"
24 OUTPUT="${outFile}" 24 OUTPUT="${outFile}"
25 HISTOGRAM_FILE="${histFile}" 25 HISTOGRAM_FILE="${histFile}"
26 DEVIATIONS="${deviations}" 26 DEVIATIONS="${deviations}"
36 36
37 VALIDATION_STRINGENCY="${validation_stringency}" 37 VALIDATION_STRINGENCY="${validation_stringency}"
38 QUIET=true 38 QUIET=true
39 VERBOSITY=ERROR 39 VERBOSITY=ERROR
40 40
41 </command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <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."/> 43 <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."/>
44 <conditional name="reference_source"> 44 <conditional name="reference_source">
45 <param name="reference_source_selector" type="select" label="Load reference genome from"> 45 <param name="reference_source_selector" type="select" label="Load reference genome from">
46 <option value="cached">Local cache</option> 46 <option value="cached">Local cache</option>
89 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" /> 89 <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
90 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/> 90 <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
91 </test> 91 </test>
92 </tests> 92 </tests>
93 93
94 <stdio>
95 <exit_code range="1:" level="fatal"/>
96 </stdio>
97 94
98 <help> 95 <help>
99 96
100 .. class:: infomark 97 .. class:: infomark
101 98