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comparison picard_CollectBaseDistributionByCycle.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
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11:efc56ee1ade4 12:05087b27692a
2 <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description> 2 <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</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( $reference_source.ref_file.fields.path )
19 #end if 19 #end if
20 20
21 java -jar \$JAVA_JAR_PATH/picard.jar 21 picard
22 CollectBaseDistributionByCycle 22 CollectBaseDistributionByCycle
23 INPUT="${inputFile}" 23 INPUT="${inputFile}"
24 OUTPUT="${outFile}" 24 OUTPUT="${outFile}"
25 CHART_OUTPUT="${pdfFile}" 25 CHART_OUTPUT="${pdfFile}"
26 ALIGNED_READS_ONLY="${aligned_reads_only}" 26 ALIGNED_READS_ONLY="${aligned_reads_only}"
30 30
31 VALIDATION_STRINGENCY="${validation_stringency}" 31 VALIDATION_STRINGENCY="${validation_stringency}"
32 QUIET=true 32 QUIET=true
33 VERBOSITY=ERROR 33 VERBOSITY=ERROR
34 34
35 </command> 35 ]]></command>
36 <inputs> 36 <inputs>
37 <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."/> 37 <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."/>
38 <conditional name="reference_source"> 38 <conditional name="reference_source">
39 <param name="reference_source_selector" type="select" label="Load reference genome from"> 39 <param name="reference_source_selector" type="select" label="Load reference genome from">
40 <option value="cached">Local cache</option> 40 <option value="cached">Local cache</option>
74 <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" /> 74 <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" />
75 <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/> 75 <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/>
76 </test> 76 </test>
77 </tests> 77 </tests>
78 78
79 <stdio>
80 <exit_code range="1:" level="fatal"/>
81 </stdio>
82 79
83 <help> 80 <help>
84 81
85 .. class:: infomark 82 .. class:: infomark
86 83