Mercurial > repos > devteam > picard1106
diff picard_FixMateInformation.xml @ 103:ae3d9a7c8399 draft
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author | devteam |
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date | Mon, 24 Feb 2014 23:29:38 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_FixMateInformation.xml Mon Feb 24 23:29:38 2014 -0500 @@ -0,0 +1,107 @@ +<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.106.0"> + <description>for paired data</description> + <command interpreter="python"> + picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}" + --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}" + </command> + <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> + <inputs> + <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix" + help="If empty, upload or import a SAM/BAM dataset."/> + <param name="sortOrder" type="select" help="If in doubt, leave as default and read Picard/Samtools documentation" + label="Sort order"> + <option value="coordinate" selected ="true">Coordinate sort</option> + <option value="queryname">Query name sort</option> + <option value="unsorted">Unsorted - docs not clear if this means unchanged or not</option> + </param> + <param name="out_prefix" value="Fix Mate" type="text" + label="Title for the output file" help="Use this remind you what the job was for." size="80" /> + <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" /> + </inputs> + <outputs> + <data format="bam" name="out_file" label="${tool.name} on ${on_string}: ${outputFormat} with fixed mates"> + <change_format> + <when input="outputFormat" value="sam" format="sam" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="picard_input_sorted_pair.sam" /> + <param name="sortOrder" value="coordinate" /> + <param name="outputFormat" value="True" /> + <param name="out_prefix" value="Test FixMate" /> + <output name="out_file" file="picard_output_fixmate_sorted_pair.bam" ftype="bam" /> + </test> + <test> + <param name="input_file" value="picard_input_sorted_pair.sam" /> + <param name="sortOrder" value="coordinate" /> + <param name="outputFormat" value="False" /> + <param name="out_prefix" value="Test FixMate" /> + <output name="out_file" file="picard_output_fixmate_sorted_pair.sam" ftype="sam" /> + </test> + </tests> + <help> + + +.. class:: infomark + +**Purpose** + +Ensure that all mate-pair information is in sync between each read and it's mate pair. + +**Picard documentation** + +This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +.. class:: warningmark + +**Useful for paired data only** + +Likely won't do anything helpful for single end sequence data +Currently, Galaxy doesn't distinguish paired from single ended SAM/BAM so make sure +the data you choose are valid (paired end) SAM or BAM data - unless you trust this +tool not to harm your data. + +----- + +.. class:: infomark + +**Syntax** + +- **Input** - a paired read sam/bam format aligned short read data in your current history +- **Sort order** - can be used to adjust the ordering of reads +- **Title** - the title to use for all output files from this job - use it for high level metadata +- **Output Format** - either SAM or compressed as BAM + +----- + +.. class:: infomark + +**Inputs, outputs, and parameters** + +.. csv-table:: + + :header-rows: 1 + + Option,Description + "INPUT=File","The input file to fix. This option may be specified 0 or more times." + "OUTPUT=File","The output file to write to" + "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}" + "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false" + +.. class:: warningmark + +**Warning on SAM/BAM quality** + +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** +flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears +to be the only way to deal with SAM/BAM that cannot be parsed. + + + </help> +</tool> + +