Mercurial > repos > bgruening > salmon
changeset 2:1b22d8a18acc draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 359ddec398e18d3e2a534239b1202691595d1243
| author | bgruening |
|---|---|
| date | Thu, 13 Apr 2017 08:18:26 -0400 |
| parents | c1d822f84e1a |
| children | 5a60f347f566 |
| files | salmon.xml test-data/reads_1.fastq.gz test-data/reads_2.fastq.gz |
| diffstat | 3 files changed, 54 insertions(+), 6 deletions(-) [+] |
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--- a/salmon.xml Thu Feb 02 19:38:01 2017 -0500 +++ b/salmon.xml Thu Apr 13 08:18:26 2017 -0400 @@ -13,6 +13,7 @@ </macros> <requirements> + <requirement type="package" version="1.0.6">bzip2</requirement> <requirement type="package" version="0.7.2">salmon</requirement> </requirements> @@ -45,10 +46,16 @@ #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 && @@ -56,6 +63,11 @@ #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 && @@ -68,10 +80,24 @@ --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 ./output @@ -168,12 +194,12 @@ <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> @@ -333,6 +359,28 @@ </assert_contents> </output> </test> + <test> <!-- gzipped input --> + <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 name="output_quant"> + <assert_contents> + <has_text text="EffectiveLength" /> + <has_text text="TPM" /> + <has_text text="NM_001168316" /> + <has_text text="NM_174914" /> + <has_text text="NM_018953" /> + <has_text text="NR_003084" /> + <has_text text="NM_017410" /> + <has_text text="NM_153693" /> + <has_text text="NR_031764" /> + <has_n_columns n="5" /> + </assert_contents> + </output> + </test> <test> <param name="single_or_paired_opts" value="paired" /> <param name="input_mate1" value="reads_1.fastq" />