Mercurial > repos > bgruening > sailfish
changeset 6:5bc9cd008ceb draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 359ddec398e18d3e2a534239b1202691595d1243
| author | bgruening |
|---|---|
| date | Thu, 13 Apr 2017 08:20:00 -0400 |
| parents | 1b4ed566a41c |
| children | a8f343909c17 |
| files | sailfish.tar.bz2 sailfish.xml test-data/reads_1.fastq.gz test-data/reads_2.fastq.gz |
| diffstat | 4 files changed, 42 insertions(+), 7 deletions(-) [+] |
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--- a/sailfish.xml Wed Nov 02 10:30:36 2016 -0400 +++ b/sailfish.xml Thu Apr 13 08:20:00 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="sailfish" name="Sailfish" version="0.10.1"> +<tool id="sailfish" name="Sailfish" version="0.10.1.1"> <description>transcript quantification from RNA-seq data</description> <macros> <xml name="strandedness"> @@ -10,6 +10,7 @@ </xml> </macros> <requirements> + <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="0.10.1">sailfish</requirement> </requirements> <stdio> @@ -33,10 +34,16 @@ #set $index_path = $refTranscriptSource.index.fields.path #end if && + #set compressed = 'no' #if $single_or_paired.single_or_paired_opts == 'single': #if $single_or_paired.input_singles.ext == 'fasta': #set $ext = 'fasta' #else: + #if $single_or_paired.input_singles.is_of_type("fastq.gz"): + #set compressed = 'GZ' + #else if $single_or_paired.input_singles.is_of_type("fastq.bz2"): + #set compressed = 'BZ2' + #end if #set $ext = 'fastq' #end if ln -s $single_or_paired.input_singles ./single.$ext && @@ -44,6 +51,11 @@ #if $single_or_paired.input_mate1.ext == 'fasta': #set $ext = 'fasta' #else: + #if $single_or_paired.input_mate1.is_of_type("fastq.gz"): + #set compressed = 'GZ' + #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2"): + #set compressed = 'BZ2' + #end if #set $ext = 'fastq' #end if ln -s $single_or_paired.input_mate1 ./mate1.$ext && @@ -56,10 +68,24 @@ --index $index_path #if $single_or_paired.single_or_paired_opts == 'single': --libType ${single_or_paired.strandedness} - --unmatedReads ./single.$ext + #if $compressed == 'GZ': + --unmatedReads <(zcat ./single.$ext) + #else if $compressed == 'BZ2': + --unmatedReads <(bzcat ./single.$ext) + #else: + --unmatedReads ./single.$ext + #end if #else: - --mates1 ./mate1.$ext - --mates2 ./mate2.$ext + #if $compressed == 'GZ': + --mates1 <(zcat ./mate1.$ext) + --mates2 <(zcat ./mate2.$ext) + #else if $compressed == 'BZ2': + --mates1 <(bzcat ./mate1.$ext) + --mates2 <(bzcat ./mate2.$ext) + #else: + --mates1 ./mate1.$ext + --mates2 ./mate2.$ext + #end if --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" #end if --output ./results @@ -138,12 +164,12 @@ <option value="paired">Paired-end</option> </param> <when value="single"> - <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." /> + <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." /> <expand macro="strandedness" /> </when> <when value="paired"> - <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." /> - <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." /> + <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." /> + <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." /> <param name="orientation" type="select" label="Relative orientation of reads within a pair"> <option value="M">Mates are oriented in the same direction (M = matching)</option> <option value="O">Mates are oriented away from each other (O = outward)</option> @@ -273,6 +299,15 @@ <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" /> </test> + <test> <!-- gzipped version of above --> + <param name="single_or_paired_opts" value="paired" /> + <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" /> + <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" /> + <param name="biasCorrect" value="False" /> + <param name="TranscriptSource" value="history" /> + <param name="ownFile" value="transcripts.fasta" ftype="fasta" /> + <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" /> + </test> <test> <param name="single_or_paired_opts" value="paired" /> <param name="input_mate1" value="reads_1.fastq" />