Mercurial > repos > chrisw > monorail_test
changeset 8:0de07638de49 draft
Uploaded
author | chrisw |
---|---|
date | Wed, 13 Feb 2019 15:29:49 -0500 |
parents | 03be34974b83 |
children | 05932011f686 |
files | monorail.xml |
diffstat | 1 files changed, 18 insertions(+), 24 deletions(-) [+] |
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--- a/monorail.xml Tue Feb 12 14:01:31 2019 -0500 +++ b/monorail.xml Wed Feb 13 15:29:49 2019 -0500 @@ -3,24 +3,28 @@ <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> --> + <requirement type="package" version="5.4.0">snakemake</requirement> + <requirement type="package" version="1.3.8">zstd</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 - $exons - ./ + <command detect_errors="aggressive"><![CDATA[ + snakemake --snakefile "$__tool_directory__/Snakefile + -j \${GALAXY_SLOTS:-4} + --config #if str($singlePaired.sPaired) == "paired_collection" - '$singlePaired.input.forward' '$singlePaired.input.reverse' + inputs="$singlePaired.input.forward,$singlePaired.input.reverse" #else - '$singlePaired.input1' + inputs="$singlePaired.input1" #if str($singlePaired.sPaired) == "paired" - '$singlePaired.input2' + inputs="$singlePaired.input1,$singlePaired.input2" #end if #end if + output="./" + temp="./tmp" + ref="$refGenomeSource.GTFconditional.genomeDir.fields.path" + genome="ath10" + exon_bed="$exons" + study="SRP182756" ]]></command> <inputs> <!-- FASTQ input(s) and options specifically for paired-end data. --> @@ -88,25 +92,15 @@ <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" /> </when> </conditional> - <param name="exons" type="data" format="bed" label="Exon annotation BED file" help="Upload/use a BED formatted list of exon intervals for quantifying"/> - <!-- <param name="exon_annotation" type="select" label="Select an exon annotation BED file" help="If your exon annotation is not listed, contact the Galaxy team"> - <options from_data_table="exon_annotations"> - <filter type="static_value" column="4" value="0"/> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> --> <param name="min_uniq_qual" type="integer" value="10" label="Minimum mapping quality for unique alignments" help="Set this to an appropriate integer value to filter out non-unique alignments"/> </inputs> - - - <!-- <expand macro="dbKeyActions" /> --> -<outputs> + <outputs> + <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/> + <!-- <data format="txt" name="output_log" label="${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 ${on_string}: chimeric junctions" from_work_dir="Chimeric.out.junction"/> <data format="interval" name="splice_junctions" label="${tool.name} on ${on_string}: splice junctions.bed" from_work_dir="SJ.out.tab"/> <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="sorted.bam"/>