view riboplot.xml @ 1:1e9797878349

remove samtools requirement and use updated pysam

<tool id="riboplot" name="riboplot" version="0.1.0">
    <description>Plot and output read counts for a single transcript in an alignment (BAM)
    </description>
    <requirements>
        <requirement type="package" version="1.2.1">matplotlib</requirement>
        <requirement type="package" version="0.7.7">pysam</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">./riboplot/riboplot.py
    --ribo_file "${ribo_file}"
    --transcriptome_fasta "${transcriptome_fasta}"
    --transcript_name "${transcript_name}"
    #if $rnacov.rnacov_select=="yes"
        --rna_file "${rna_file}"
    #end if
    --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="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
            <validator type="empty_field" message="Field requires a value"/>
            <sanitizer>
                <valid>
                    <add value="|"/>
                </valid>
            </sanitizer>
        </param>
        <conditional name="rnacov">
            <param name="rnacov_select" type="select" label="Include RNA Coverage">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
            </when>
        </conditional>
        <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="riboplot (HTML report)"/>
    </outputs>
    <help>
    </help>
</tool>