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/tools/picard/rgPicardFixMate.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0">
  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 "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/FixMateInformation.jar" --sortorder "$sortOrder"
  6  </command>
  7  <requirements><requirement type="package">picard</requirement></requirements>
  8  <inputs>
  9    <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix"
 10      help="If empty, upload or import a SAM/BAM dataset."/>
 11      <param name="sortOrder" type="select" help="If in doubt, leave as default and read Picard/Samtools documentation"
 12         label="Sort order">
 13        <option value="coordinate" selected ="true">Coordinate sort</option>
 14        <option value="queryname">Query name sort</option>
 15        <option value="unsorted">Unsorted - docs not clear if this means unchanged or not</option>
 16      </param>
 17    <param name="out_prefix" value="Fix Mate" type="text"
 18      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
 19    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
 20  </inputs>
 21  <outputs>
 22    <data format="bam" name="out_file" label="${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
 51Ensure that all mate-pair information is in sync between each read and it's mate pair.
 52
 53**Picard documentation**
 54
 55This 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
 63Likely won't do anything helpful for single end sequence data
 64Currently, Galaxy doesn't distinguish paired from single ended SAM/BAM so make sure
 65the data you choose are valid (paired end) SAM or BAM data - unless you trust this
 66tool 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
 99Many 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**
100flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
101to be the only way to deal with SAM/BAM that cannot be parsed.
102
103
104  </help>
105</tool>
106
107