Mercurial > repos > brenninc > pairedbamtobed12
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author | brenninc |
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date | Tue, 10 May 2016 12:43:27 -0400 |
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<tool id="pairedbamtobed12" name="Paired bam to bed12" version="0.1"> <description>Paired Bam to Bed. With samtools sorting by name beforehand and back to required order for galaxy afterwards.</description> <requirements> <requirement type="package" version="1.0">pairedbamtobed12</requirement> <requirement type="package" version="1.2">samtools</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <command> <![CDATA[ samtools sort -n -O bam -T by_name -o sorted_by_name.bam "${input}" ; pairedBamToBed12 -i sorted_by_name.bam > "${output}" ]]> </command> <inputs> <param name="input" format="bam" label="Select BAM dataset to convert to bed" type="data" /> </inputs> <outputs> <data format="bed" name="output" label="Bed12 version of ${on_string}" /> </outputs> <tests> <!-- test data too large for toolshed See: https://github.com/Christian-B/galaxy_shedtools/tree/master/pairedBamToBed12 --> <!--test> <param ftype="bam" name="input" value="filtered.bam" /> <output file="paired.bed" ftype="bed" name="output" /> </test--> </tests> <help> <![CDATA[ This tools runs pairedbamtobed12 to convert a paired bam file to a bed file. As pairedbamtobed12 requires a bam file sorted by name, while galaxy only allows ones sorted by alignment this tool first uses Samtools to reorder the bam file. ]]> </help> <citations> <citation type="bibtex"> @misc{ pairedBamToBed12, author = {Nicolas Bertin, Mickaƫl Mendez, Charles Plessy}, title = {pairedBamToBed12 on GitHub}, url = {https://github.com/Population-Transcriptomics/pairedBamToBed12} } </citation> </citations> </tool>