view ribocount.xml @ 1:1e9797878349

remove samtools requirement and use updated pysam

<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>