comparison riboplot.xml @ 2:b6fd86c539ea

Fix pysam version in riboplot (was 0.7.7 instead of 0.8.3). Fix move sys import to the top in ribocount.py, riboplot.py. Minor: * Include an empty conditional when no RNA coverage is required. * Remove output directories after zip file is created.

1:1e9797878349

<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}"

                <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>

2:b6fd86c539ea

<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="0.8.3">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}"

                <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>
            <when value="no" />
        </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>