comparison riboplot.xml @ 42:abab200b808b draft default tip

Uploaded

41:45f5550a0aa3

<tool id="riboplot" name="riboplot" version="0.2.5">
    <description>Plot and output read counts for a single transcript in an alignment (BAM)
    </description>
    <requirements>
        <requirement type="package" version="0.2.5">riboplot</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <command>python \${RIBOPLOT_PATH}/riboplot
    --ribo_file "${ribo_file}"
    --transcriptome_fasta "${transcriptome_fasta}"
    --transcript_name "${transcript_name}"
    #if $rnacov.rnacov_select=="yes"
        --rna_file "${rna_file}"

    </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>

42:abab200b808b

<tool id="riboplot" name="riboplot" version="0.3.1">
    <description>Plot and output read counts for a single transcript in an alignment (BAM)
    </description>
    <requirements>
        <requirement type="package" version="0.3.1">riboplot</requirement>
     </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <command>riboplot
    --ribo_file "${ribo_file}"
    --transcriptome_fasta "${transcriptome_fasta}"
    --transcript_name "${transcript_name}"
    #if $rnacov.rnacov_select=="yes"
        --rna_file "${rna_file}"

    </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>