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<tool id="monorail" name="Run the Monorail RNA-seq analysis pipeline" version="0.1.0">
    <!-- much of this was based on https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rnaStar.xml -->
    <requirements>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="2.7.3a">star</requirement>
        <requirement type="package" version="0.4.0">bamcount</requirement>
        <requirement type="package" version="5.4.0">snakemake-minimal</requirement>
        <requirement type="package" version="1.3.3">zstd</requirement>
        <requirement type="package" version="1.3">seqtk</requirement>
<!--
        <requirement type="package" version="2.1.0">hisat2</requirement>
        <requirement type="package" version="0.8">fastq-tools</requirement>
        <requirement type="package" version="0.12.0">salmon</requirement>
        <requirement type="package" version="0.5.0">regtools</requirement>
        <requirement type="package" version="2.9.1">sra-tools</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[
            $__tool_directory__/run_mr_snakemake.sh "$__tool_directory__/Snakefile"
            \${GALAXY_SLOTS:-4} 
                    "$index_source.fields.path"
                    "$index_source.fields.path/$index_source.fields.name/gtf/exons.bed"
                    "."
                    "./tmp"
                    "$index_source.fields.name"
                    #if str($singlePaired.sPaired) == "paired_collection"
                        "$singlePaired.input.forward,$singlePaired.input.reverse"
                        #if $singlePaired.input.forward.is_of_type("fastq.gz"):
                            "compressed=1"
                        #end if
                    #else
                        "$singlePaired.input1"
                        #if str($singlePaired.sPaired) == "paired"
                            inputs="$singlePaired.input1,$singlePaired.input2"
                        #end if
                        #if $singlePaired.input1.is_of_type("fastq.gz"):
                            "compressed=1"
                        #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. -->
                        <param name="index_source" type="select" label="Select reference genome index set" help="If your genome of interest is not listed, contact the Galaxy team">
                            <options from_data_table="monorail_index">
                                <filter type="sort_by" column="2" />
                                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                            </options>
                        </param>
    </inputs>
    <outputs>
        <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/>
        <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="SJ.out.tab"/>
        <!-- 
        <data format="txt" name="frag" label="${tool.name} on ${on_string}: Fragment Distribution" from_work_dir="bamcount_frag.tsv"/>
        <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"/>
        <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bc.auc.tsv"/>
        <data format="txt" name="bc_log" label="${tool.name} on ${on_string}: bamcount log" from_work_dir="bc.log"/>
        <data format="interval" name="chimeric_junctions" label="${tool.name} on ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"/>
        <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="sorted.bam"/>
        <data name="mapped_reads_index" format="bai" label="${tool.name} on ${on_string}: mapped.bam.bai" from_work_dir="sorted.bam.bai"/>
        -->
    </outputs>
    <help>
        Run the Monorail RNA-seq analysis pipeline
    </help>
</tool>