Mercurial > repos > devteam > picard
annotate rgPicardFixMate.xml @ 4:ab1f60c26526 draft
Uploaded valid tools and complex repository dependency definition.
| author | devteam |
|---|---|
| date | Fri, 21 Feb 2014 12:07:49 -0500 |
| parents | 9227b8c3093b |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0"> |
| 2 <description>for paired data</description> | |
| 3 <command interpreter="python"> | |
|
2
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
4 picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}" |
|
9227b8c3093b
Updated command line format per dev team standards.
devteam <devteam@galaxyproject.org>
parents:
0
diff
changeset
|
5 --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}" |
| 0 | 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 |