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comparison picard_RevertOriginalBaseQualitiesAndAddMateCigar.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
equal deleted inserted replaced
11:efc56ee1ade4 12:05087b27692a
2 <description>revert the original base qualities and add the mate cigar tag</description> 2 <description>revert the original base qualities and add the mate cigar tag</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 RevertOriginalBaseQualitiesAndAddMateCigar 11 RevertOriginalBaseQualitiesAndAddMateCigar
12 12
13 INPUT="${inputFile}" 13 INPUT="${inputFile}"
14 OUTPUT="${outFile}" 14 OUTPUT="${outFile}"
15 15
19 SORT_ORDER=coordinate 19 SORT_ORDER=coordinate
20 VALIDATION_STRINGENCY="${validation_stringency}" 20 VALIDATION_STRINGENCY="${validation_stringency}"
21 QUIET=true 21 QUIET=true
22 VERBOSITY=ERROR 22 VERBOSITY=ERROR
23 23
24 </command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <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"/> 26 <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"/>
27 <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"/> 27 <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"/>
28 <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/> 28 <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>
29 29
39 <test> 39 <test>
40 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> 40 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
41 <param name="restore_original_qualities" value="True"/> 41 <param name="restore_original_qualities" value="True"/>
42 <param name="max_records_to_examine" value="10000"/> 42 <param name="max_records_to_examine" value="10000"/>
43 <param name="validation_stringency" value="LENIENT"/> 43 <param name="validation_stringency" value="LENIENT"/>
44 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/> 44 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
45 </test> 45 </test>
46 </tests> 46 </tests>
47 47
48 <stdio>
49 <exit_code range="1:" level="fatal"/>
50 </stdio>
51 48
52 <help> 49 <help>
53 50
54 **Purpose** 51 **Purpose**
55 52