comparison create_ribosome_profile/create_ribosome_profile.xml @ 4:49e8fcbaaa72 draft

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3:dfed3b7be399

<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.a">
    <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description>
    <requirements>
        <requirement type="package" version="1.73">biopython</requirement>
        <requirement type="package" version="0.19.0">pysam</requirement>
    </requirements>
    <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4} ${output1}</command>
    <inputs>
        <param name="input1" type="data" format="bam" label="BAM file to process"/>
        <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
        <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
        <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
            <option value="offset" selected="true">Use offset approach</option>
            <option value="weight">Use weight centered approach</option>
        </param>

4:49e8fcbaaa72

<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.1">
    <description>Produce a sorted bed file of A-Site profiles of RPFs.</description>
    <requirements>
        <requirement type="package" version="1.79">biopython</requirement>
        <requirement type="package" version="0.19.0">pysam</requirement>
    </requirements>
    <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} $refGenomeSource.genomeSource
            #if $refGenomeSource.genomeSource == "builtin":
                none ${refGenomeSource.input1_builtin.fields.path} ${input4} ${output1}
            #else:
                ${refGenomeSource.input1_file} none ${input4} ${output1}
            #end if
    </command>
    <inputs>
        <param name="input1" type="data" format="bam" label="BAM file to process"/>
        <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
        <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
            <option value="builtin">Use a built-in FASTA</option>
            <option value="history">Use one from the history</option>
        </param>
        <when value="builtin">
            <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
                <options from_data_table="builtin_fastas">
                    <filter type="sort_by" column="2" />
                    <validator type="no_options" message="No built-ins are available" />
                </options>
            </param>
        </when>
        <when value="history">
            <param name="input1_file" type="data" format="fasta" label="FASTA File" />
        </when>
        <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
        <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
            <option value="offset" selected="true">Use offset approach</option>
            <option value="weight">Use weight centered approach</option>
        </param>