Mercurial > repos > chrisw > monorail_test
changeset 1:5c92c1163a6d draft
Uploaded
author | chrisw |
---|---|
date | Tue, 12 Feb 2019 11:08:02 -0500 |
parents | a25fa2b5e379 |
children | f0c744144100 |
files | monorail.xml |
diffstat | 1 files changed, 122 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/monorail.xml Tue Feb 12 11:08:02 2019 -0500 @@ -0,0 +1,122 @@ +<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="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>