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comparison picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
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 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 picard 10 picard RevertOriginalBaseQualitiesAndAddMateCigar
11 RevertOriginalBaseQualitiesAndAddMateCigar
12 11
13 INPUT='$inputFile' 12 --INPUT '$inputFile'
14 OUTPUT="${outFile}" 13 --OUTPUT '${outFile}'
15 14
16 RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" 15 --RESTORE_ORIGINAL_QUALITIES '${restore_original_qualities}'
17 MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}" 16 --MAX_RECORDS_TO_EXAMINE '${max_records_to_examine}'
18 17
19 SORT_ORDER=coordinate 18 --SORT_ORDER coordinate
20 VALIDATION_STRINGENCY="${validation_stringency}" 19 --VALIDATION_STRINGENCY '${validation_stringency}'
21 QUIET=true 20 --QUIET true
22 VERBOSITY=ERROR 21 --VERBOSITY ERROR
23 22
24 ]]></command> 23 ]]></command>
25 <inputs> 24 <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"/> 25 <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"/> 26 <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"/> 27 <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 28 <expand macro="VS"/>
30 <expand macro="VS" /> 29 </inputs>
31 30 <outputs>
32 </inputs> 31 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
33 32 </outputs>
34 <outputs> 33 <tests>
35 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> 34 <test>
36 </outputs> 35 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
37 36 <param name="restore_original_qualities" value="True"/>
38 <tests> 37 <param name="max_records_to_examine" value="10000"/>
39 <test> 38 <param name="validation_stringency" value="LENIENT"/>
40 <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> 39 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
41 <param name="restore_original_qualities" value="True"/> 40 </test>
42 <param name="max_records_to_examine" value="10000"/> 41 </tests>
43 <param name="validation_stringency" value="LENIENT"/> 42 <help>
44 <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="4"/>
45 </test>
46 </tests>
47
48
49 <help>
50 43
51 **Purpose** 44 **Purpose**
52 45
53 Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs. 46 Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs.
54 47
65 cigars exist. Set to 0 to never skip the file. Default value: 10000. 58 cigars exist. Set to 0 to never skip the file. Default value: 10000.
66 59
67 @more_info@ 60 @more_info@
68 61
69 </help> 62 </help>
70 <expand macro="citations" /> 63 <expand macro="citations"/>
71 </tool> 64 </tool>