view monorail.xml @ 5:d2d9937d1f9c draft

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<tool id="monorail" name="Run the Monorail RNA-seq analysis pipeline" version="0.1.0">
    <requirements>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="2.6.0b">star</requirement>
        <requirement type="package" version="0.2.6">bamcount</requirement>
        <!-- <requirement type="package" version="5.4.0">snakemake-minimal</requirement> -->
    </requirements>
        <!-- /bin/bash -x monorail.slim.sh ../ath10 4 10 ../ath10/gtf/exons.bed ./tmp2 ../fastqs/SRR8505407_1_100.fastq.gz ../fastqs/SRR8505407_2_100.fastq.gz -->
     <command detect_errors="aggressive"><![CDATA[
                /bin/bash -x "$__tool_directory__/monorail.sh"
                    $refGenomeSource.GTFconditional.genomeDir.fields.path
                    \${GALAXY_SLOTS:-4}
                    $min_uniq_qual
                    $exons
                    ./
                    #if str($singlePaired.sPaired) == "paired_collection"
                        '$singlePaired.input.forward' '$singlePaired.input.reverse'
                    #else
                        '$singlePaired.input1'
                        #if str($singlePaired.sPaired) == "paired"
                            '$singlePaired.input2'
                        #end if
                    #end if
    ]]></command>
        <inputs>
 <!-- FASTQ input(s) and options specifically for paired-end data. -->
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Single-end or paired-end reads">
                <option value="single" selected="true">Single-end</option>
                <option value="paired">Paired-end (as individual datasets)</option>
                <option value="paired_collection">Paired-end (as collection)</option>
            </param>
            <when value="single">
                <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file"/>
            </when>
            <when value="paired">
                <param format="fastq,fastq.gz" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads"/>
                <param format="fastq,fastq.gz" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"/>
            </when>
            <when value="paired_collection">
                <param format="fastq,fastq.gz" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads"/>
            </when>
        </conditional>
       
        <!-- 
        <param name="refGenomeSource" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                            <options from_data_table="rnastar_index2">
                                <filter type="static_value" column="4" value="0"/>
                                <filter type="sort_by" column="2" />
                                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                            </options>
        </param>
        -->

 <!-- Genome source. -->
        <conditional name="refGenomeSource">
            <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
                <option value="indexed" selected="True">Use a built-in index</option>
                <option value="history">Use reference genome from history and create temporary index</option>
            </param>
            <when value="indexed">
                <conditional name="GTFconditional">
                    <param name="GTFselect" type="select" label="Reference genome with or without an annotation" help="Must the index have been created WITH a GTF file (if not you can specify one afterward).">
                        <option value="without-gtf">use genome reference without builtin gene-model</option>
                        <option value="with-gtf">use genome reference with builtin gene-model</option>
                    </param>
                    <when value="with-gtf">
                        <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                            <options from_data_table="rnastar_index2">
                                <filter type="static_value" column="4" value="1"/>
                                <filter type="sort_by" column="2" />
                                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                            </options>
                        </param>
                    </when>
                    <when value="without-gtf">
                        <param name="genomeDir" argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                            <options from_data_table="rnastar_index2">
                                <filter type="static_value" column="4" value="0"/>
                                <filter type="sort_by" column="2" />
                                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                            </options>
                        </param>
                    </when>
                </conditional>
            </when>
            <when value="history">
                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
            </when>
        </conditional>

        <param name="exons" type="data" format="bed" label="Exon annotation BED file" help="Upload/use a BED formatted list of exon intervals for quantifying"/>
        <!-- <param name="exon_annotation" type="select" label="Select an exon annotation BED file" help="If your exon annotation is not listed, contact the Galaxy team">
                            <options from_data_table="exon_annotations">
                                <filter type="static_value" column="4" value="0"/>
                                <filter type="sort_by" column="2" />
                                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                            </options>
        </param> -->
        <param name="min_uniq_qual" type="integer" value="10" label="Minimum mapping quality for unique alignments" help="Set this to an appropriate integer value to filter out non-unique alignments"/>
        </inputs>
    

        <!--    <expand macro="dbKeyActions" /> -->
<outputs>
        <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
        </data>
        <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction">
        </data>

        <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab">
        </data>
        <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="sorted.bam">
        </data>
        <data name="mapped_reads_index" format="bai" label="${tool.name} on ${on_string}: mapped.bam.bai" from_work_dir="sorted.bam.bai">
        </data>
    </outputs>
    <help>
        Run the Monorail RNA-seq analysis pipeline
    </help>
</tool>