Mercurial > repos > vimalkumarvelayudhan > riboplot
view ribocount.xml @ 7:096c6bbf4a04
Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
author | Vimalkumar Velayudhan <vimal@biotechcoder.com> |
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date | Thu, 13 Aug 2015 15:03:20 +0100 |
parents | 1901dcdc12ff |
children | 844eb8c36f32 |
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<tool id="ribocount" name="ribocount" version="0.1.0"> <description>Get read counts for all transcripts in an alignment (BAM) </description> <requirements> <requirement type="package" version="0.8.3">pysam</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error" /> </stdio> <command interpreter="python">riboplot/ribocount.py --ribo_file "${ribo_file}" --transcriptome_fasta "${transcriptome_fasta}" --read_length "${read_length}" --read_offset "${read_offset}" --html_file "${html_file}" --output_path "${html_file.files_path}" ## --debug </command> <inputs> <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/> <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/> <param name="read_length" type="integer" label="Read length to consider" value="28"/> <param name="read_offset" type="integer" label="Offset" value="0"/> </inputs> <outputs> <data format="html" name="html_file" label="ribocount (HTML report)"/> </outputs> <help> </help> </tool>