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comparison picard_MergeSamFiles.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
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
2 <description>merges multiple SAM/BAM datasets into one</description> 2 <description>merges multiple SAM/BAM datasets into one</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 9
10 java -jar \$JAVA_JAR_PATH/picard.jar 10 picard
11 MergeSamFiles 11 MergeSamFiles
12 12
13 #for $element in $inputFile: 13 #for $element in $inputFile:
14 INPUT="${element}" 14 INPUT="${element}"
15 #end for 15 #end for
26 SORT_ORDER=coordinate 26 SORT_ORDER=coordinate
27 VALIDATION_STRINGENCY="${validation_stringency}" 27 VALIDATION_STRINGENCY="${validation_stringency}"
28 QUIET=true 28 QUIET=true
29 VERBOSITY=ERROR 29 VERBOSITY=ERROR
30 30
31 </command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 33 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
34 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> 34 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
35 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/> 35 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
36 36
50 <test> 50 <test>
51 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/> 51 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
52 <param name="assume_sorted" value="False"/> 52 <param name="assume_sorted" value="False"/>
53 <param name="merge_sequence_dictionaries" value="False"/> 53 <param name="merge_sequence_dictionaries" value="False"/>
54 <param name="validation_stringency" value="LENIENT"/> 54 <param name="validation_stringency" value="LENIENT"/>
55 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/> 55 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/>
56 </test> 56 </test>
57 </tests> 57 </tests>
58 58
59 <stdio>
60 <exit_code range="1:" level="fatal"/>
61 </stdio>
62 59
63 <help> 60 <help>
64 61
65 **Purpose** 62 **Purpose**
66 63