Mercurial > repos > chrisw > monorail_test
changeset 15:3fa68a0d59c5 draft
Uploaded
author | chrisw |
---|---|
date | Wed, 13 Feb 2019 17:03:56 -0500 |
parents | f2258de365ee |
children | d2770bc432e1 |
files | Snakefile monorail.xml |
diffstat | 2 files changed, 14 insertions(+), 10 deletions(-) [+] |
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--- a/Snakefile Wed Feb 13 16:05:41 2019 -0500 +++ b/Snakefile Wed Feb 13 17:03:56 2019 -0500 @@ -57,13 +57,13 @@ i = 1 for f in fastqs: newf = '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, i) - run_command(['zcat',f,'>',newf]) + if 'compressed' in config: + run_command(['zcat',f,'>',newf]) + else: + os.symlink(os.path.abspath(f), newf) #create fastq 0 if i == 1: - try: - os.symlink(os.path.abspath(newf), '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 0)) - except FileExistsError as fee: - pass + os.symlink(os.path.abspath(newf), '%s/%s_%s_%s_%s_%d.fastq' % (config['temp'], run_acc, study_acc, genome, method, 0)) i += 1 #create fastq 2 if not paired if i == 2:
--- a/monorail.xml Wed Feb 13 16:05:41 2019 -0500 +++ b/monorail.xml Wed Feb 13 17:03:56 2019 -0500 @@ -1,4 +1,5 @@ <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="2.6.0b">star</requirement> @@ -13,18 +14,22 @@ --config #if str($singlePaired.sPaired) == "paired_collection" inputs="$singlePaired.input.forward,$singlePaired.input.reverse" + #if $singlePaired.input.forward.is_of_type("fastq.gz"): + compressed=1 + #end if #else inputs="$singlePaired.input1" #if str($singlePaired.sPaired) == "paired" inputs="$singlePaired.input1,$singlePaired.input2" #end if + #if $singlePaired.input1.is_of_type("fastq.gz"): + compressed=1 + #end if #end if + ref="$refGenomeSource.GTFconditional.genomeDir.fields.path" + exon_bed="$exons" output="." temp="./tmp" - ref="$refGenomeSource.GTFconditional.genomeDir.fields.path" - genome="ath10" - exon_bed="$exons" - study="SRP182756" ]]></command> <inputs> <!-- FASTQ input(s) and options specifically for paired-end data. --> @@ -93,7 +98,6 @@ </when> </conditional> <param name="exons" type="data" format="bed" label="Exon annotation BED file" help="Upload/use a BED formatted list of exon intervals for quantifying"/> - <param name="min_uniq_qual" type="integer" value="10" label="Minimum mapping quality for unique alignments" help="Set this to an appropriate integer value to filter out non-unique alignments"/> </inputs> <outputs> <data format="txt" name="auc" label="${tool.name} on ${on_string}: AUC" from_work_dir="bamcount_auc.tsv"/>