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comparison picard_RevertSam.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 5eaa8a968300
children 7e6fd3d0f16e
comparison
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
2 <description>revert SAM/BAM datasets to a previous state</description> 2 <description>revert SAM/BAM datasets to a previous state</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 RevertSam 11 RevertSam
12 12
13 INPUT="${inputFile}" 13 INPUT="${inputFile}"
14 OUTPUT="${outFile}" 14 OUTPUT="${outFile}"
15 15
29 SORT_ORDER="${sort_order}" 29 SORT_ORDER="${sort_order}"
30 VALIDATION_STRINGENCY="${validation_stringency}" 30 VALIDATION_STRINGENCY="${validation_stringency}"
31 QUIET=true 31 QUIET=true
32 VERBOSITY=ERROR 32 VERBOSITY=ERROR
33 33
34 </command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <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"/> 36 <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"/>
37 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/> 37 <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
38 <param name="remove_duplicate_information" type="boolean" checked="True" label="Remove duplicate read flags from all reads" help="REMOVE_DUPLICATE_INFORMATION; Note that if this is true and REMOVE_ALIGNMENT_INFORMATION is set to False, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates; default=True"/> 38 <param name="remove_duplicate_information" type="boolean" checked="True" label="Remove duplicate read flags from all reads" help="REMOVE_DUPLICATE_INFORMATION; Note that if this is true and REMOVE_ALIGNMENT_INFORMATION is set to False, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates; default=True"/>
39 <param name="remove_alignment_information" type="boolean" checked="True" label="Remove all alignment information from the file" help="REMOVE_ALIGNMENT_INFORMATION; default=True"/> 39 <param name="remove_alignment_information" type="boolean" checked="True" label="Remove all alignment information from the file" help="REMOVE_ALIGNMENT_INFORMATION; default=True"/>
68 <param name="max_discard_fraction" value="0.01"/> 68 <param name="max_discard_fraction" value="0.01"/>
69 <param name="sample_alias" value="null"/> 69 <param name="sample_alias" value="null"/>
70 <param name="library_name" value="null"/> 70 <param name="library_name" value="null"/>
71 <param name="sort_order" value="coordinate"/> 71 <param name="sort_order" value="coordinate"/>
72 <param name="validation_stringency" value="LENIENT"/> 72 <param name="validation_stringency" value="LENIENT"/>
73 <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="2"/> 73 <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="4"/>
74 </test> 74 </test>
75 </tests> 75 </tests>
76 76
77 <stdio>
78 <exit_code range="1:" level="fatal"/>
79 </stdio>
80 77
81 <help> 78 <help>
82 79
83 **Purpose** 80 **Purpose**
84 81