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comparison picard_SamToFastq.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 2589e6207cb4
children e417b1d6288d
comparison
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6:961236c5ec73 7:08f69add4d06
2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description> 2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</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 8
9 echo "BAM" > $report &amp;&amp; ## This is necessary for output dataset detection (see output tags below) 9 echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below)
10 10
11 @java_options@ 11 @java_options@
12 12
13 java -jar \$JAVA_JAR_PATH/picard.jar 13 picard
14 SamToFastq 14 SamToFastq
15 15
16 INPUT="${inputFile}" 16 INPUT="${inputFile}"
17 17
18 #if str( $output_per_rg ) == "true": 18 #if str( $output_per_rg ) == "true":
48 48
49 VALIDATION_STRINGENCY="${validation_stringency}" 49 VALIDATION_STRINGENCY="${validation_stringency}"
50 QUIET=true 50 QUIET=true
51 VERBOSITY=ERROR 51 VERBOSITY=ERROR
52 52
53 </command> 53 ]]></command>
54 <inputs> 54 <inputs>
55 55
56 <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"/> 56 <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"/>
57 <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/> 57 <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/>
58 <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/> 58 <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/>
98 <discovered_dataset designation="INTERLEAVED" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/> 98 <discovered_dataset designation="INTERLEAVED" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
99 </output> 99 </output>
100 </test> 100 </test>
101 </tests> 101 </tests>
102 102
103 <stdio>
104 <exit_code range="1:" level="fatal"/>
105 </stdio>
106 103
107 <help> 104 <help>
108 105
109 **Purpose** 106 **Purpose**
110 107