Mercurial > repos > devteam > picard

comparison picard_CollectAlignmentSummaryMetrics.xml @ 7:08f69add4d06 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 2589e6207cb4
children e417b1d6288d
comparison
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
2 <description>writes a file containing summary alignment metrics</description> 2 <description>writes a file containing summary alignment metrics</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 <stdio> 7 <command detect_errors="exit_code"><![CDATA[
8 <exit_code range="1:" level="fatal"/>
9 </stdio>
10 <command>
11 @java_options@ 8 @java_options@
12 ##set up input files 9 ##set up input files
13 10
14 #set $reference_fasta_filename = "localref.fa" 11 #set $reference_fasta_filename = "localref.fa"
15 12
16 #if str( $reference_source.reference_source_selector ) == "history": 13 #if str( $reference_source.reference_source_selector ) == "history":
17 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 14 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
18 #else: 15 #else:
19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 16 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
20 #end if 17 #end if
21 18
22 java -jar \$JAVA_JAR_PATH/picard.jar 19 picard
23 CollectAlignmentSummaryMetrics 20 CollectAlignmentSummaryMetrics
24 INPUT="${inputFile}" 21 INPUT="${inputFile}"
25 OUTPUT="${outFile}" 22 OUTPUT="${outFile}"
26 MAX_INSERT_SIZE=${maxinsert} 23 MAX_INSERT_SIZE=${maxinsert}
27 #for $sequence in $adapters: 24 #for $sequence in $adapters:
38 35
39 VALIDATION_STRINGENCY="${validation_stringency}" 36 VALIDATION_STRINGENCY="${validation_stringency}"
40 QUIET=true 37 QUIET=true
41 VERBOSITY=ERROR 38 VERBOSITY=ERROR
42 39
43 </command> 40 ]]></command>
44 <inputs> 41 <inputs>
45 <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."/> 42 <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."/>
46 <conditional name="reference_source"> 43 <conditional name="reference_source">
47 <param name="reference_source_selector" type="select" label="Load reference genome from"> 44 <param name="reference_source_selector" type="select" label="Load reference genome from">
48 <option value="cached">Local cache</option> 45 <option value="cached">Local cache</option>