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comparison rgPicardFixMate.xml @ 4:f4d018471628 draft default tip

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author jpruab
date Tue, 13 Aug 2013 12:09:14 -0400
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3:08b477977410 4:f4d018471628
1 <tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0">
2 <description>for paired data</description>
3 <command interpreter="python">
4 picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}"
5 --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}"
6 </command>
7 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
8 <inputs>
9 <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix"
10 help="If empty, upload or import a SAM/BAM dataset."/>
11 <param name="sortOrder" type="select" help="If in doubt, leave as default and read Picard/Samtools documentation"
12 label="Sort order">
13 <option value="coordinate" selected ="true">Coordinate sort</option>
14 <option value="queryname">Query name sort</option>
15 <option value="unsorted">Unsorted - docs not clear if this means unchanged or not</option>
16 </param>
17 <param name="out_prefix" value="Fix Mate" type="text"
18 label="Title for the output file" help="Use this remind you what the job was for." size="80" />
19 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
20 </inputs>
21 <outputs>
22 <data format="bam" name="out_file" label="${tool.name} on ${on_string}: ${outputFormat} with fixed mates">
23 <change_format>
24 <when input="outputFormat" value="sam" format="sam" />
25 </change_format>
26 </data>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input_file" value="picard_input_sorted_pair.sam" />
31 <param name="sortOrder" value="coordinate" />
32 <param name="outputFormat" value="True" />
33 <param name="out_prefix" value="Test FixMate" />
34 <output name="out_file" file="picard_output_fixmate_sorted_pair.bam" ftype="bam" />
35 </test>
36 <test>
37 <param name="input_file" value="picard_input_sorted_pair.sam" />
38 <param name="sortOrder" value="coordinate" />
39 <param name="outputFormat" value="False" />
40 <param name="out_prefix" value="Test FixMate" />
41 <output name="out_file" file="picard_output_fixmate_sorted_pair.sam" ftype="sam" />
42 </test>
43 </tests>
44 <help>
45
46
47 .. class:: infomark
48
49 **Purpose**
50
51 Ensure that all mate-pair information is in sync between each read and it's mate pair.
52
53 **Picard documentation**
54
55 This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_.
56
57 .. _Picard-tools: http://www.google.com/search?q=picard+samtools
58
59 .. class:: warningmark
60
61 **Useful for paired data only**
62
63 Likely won't do anything helpful for single end sequence data
64 Currently, Galaxy doesn't distinguish paired from single ended SAM/BAM so make sure
65 the data you choose are valid (paired end) SAM or BAM data - unless you trust this
66 tool not to harm your data.
67
68 -----
69
70 .. class:: infomark
71
72 **Syntax**
73
74 - **Input** - a paired read sam/bam format aligned short read data in your current history
75 - **Sort order** - can be used to adjust the ordering of reads
76 - **Title** - the title to use for all output files from this job - use it for high level metadata
77 - **Output Format** - either SAM or compressed as BAM
78
79 -----
80
81 .. class:: infomark
82
83 **Inputs, outputs, and parameters**
84
85 .. csv-table::
86
87 :header-rows: 1
88
89 Option,Description
90 "INPUT=File","The input file to fix. This option may be specified 0 or more times."
91 "OUTPUT=File","The output file to write to"
92 "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}"
93 "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false"
94
95 .. class:: warningmark
96
97 **Warning on SAM/BAM quality**
98
99 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
100 flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
101 to be the only way to deal with SAM/BAM that cannot be parsed.
102
103
104 </help>
105 </tool>
106
107