Mercurial > repos > devteam > picard1106
diff picard_SamFormatConverter.xml @ 21:c2f6ec2fee7e draft
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author | devteam |
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date | Tue, 11 Feb 2014 18:42:41 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_SamFormatConverter.xml Tue Feb 11 18:42:41 2014 -0500 @@ -0,0 +1,74 @@ +<tool name="Picard SAM Format Converter" id="picard_SFC" version="0.1.0"> + <requirements><requirement type="package">picard</requirement></requirements> + <command interpreter="python"> + picard_wrapper.py + --input="$inputFile" + --output-format=$outputFormat + --output=$outFile + -j "\$JAVA_JAR_PATH/SamFormatConverter.jar" + </command> + <inputs> + <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM" + help="If empty, upload or import a SAM/BAM dataset." /> + <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output bam instead of sam" help="Uncheck for sam output"/> + </inputs> + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with read groups replaced"> + <change_format> + <when input="outputFormat" value="sam" format="sam" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <!-- Command for replacing read groups in bam: +java -jar SamFormatConverter.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_SFC_input1.sam O=picard_SFC_output1.samĀ· +--> + <param name="inputFile" value="picard_ARRG_input1.bam" /> + <param name="outputFormat" value="False" /> + <output name="outFile" file="picard_ARRG_output1.sam" ftype="sam" /> + </test> + <test> + <!-- Command for replacing read groups in sam: +java -jar AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_ARRG_input1.sam O=picard_ARRG_output2.sam RGLB=LIB RGPL=IL RGPU=PL +picard_ARRG_input1.bam can be created from picard_ARRG_input1.sam +--> + <param name="inputFile" value="picard_ARRG_input1.sam" /> + <output name="outFile" file="picard_ARRG_output2.sam" ftype="sam" /> + </test> + </tests> + <help> + +.. class:: infomark + +**Purpose** + +Convert a BAM file to a SAM file, or BAM to SAM. + +This is a Galaxy wrapper for SamFormatConverter, a part of the external package Picard-tools_. + + .. _Picard-tools: http://www.google.com/search?q=picard+samtools + +------ + +.. class:: infomark + +**Inputs, outputs, and parameters** + +Either a sam file or a bam file must be supplied. If a bam file is used, it must +be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. + +The output file is either bam (the default) or sam, according to user selection, +and contains the same information as the input file except for the appropraite +additional (or modified) read group tags. Bam is recommended since it is smaller. + +**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> +