# HG changeset patch # User bgruening # Date 1525949308 14400 # Node ID 885d11dc8090c331749bd997d2901699133608dc # Parent 53e9709776a0da7c37013bf34a98b069095f4a71 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit e42ab88387f117f726cfa874c6232afd2c844c86 diff -r 53e9709776a0 -r 885d11dc8090 salmon.xml --- a/salmon.xml Wed Jul 12 14:05:10 2017 -0400 +++ b/salmon.xml Thu May 10 06:48:28 2018 -0400 @@ -10,12 +10,20 @@ - 0.8.2 + + + + + + + + 0.9.1 bzip2 salmon + seqtk @@ -52,27 +60,52 @@ #if $single_or_paired.input_singles.ext == 'fasta': #set $ext = 'fasta' #else: - #if $single_or_paired.input_singles.is_of_type('fastq.gz'): + #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"): #set compressed = 'GZ' - #else if $single_or_paired.input_singles.is_of_type('fastq.bz2'): + #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set compressed = 'BZ2' #end if #set $ext = 'fastq' #end if ln -s $single_or_paired.input_singles ./single.$ext && - #else: + #else if $single_or_paired.single_or_paired_opts == 'paired': #if $single_or_paired.input_mate1.ext == 'fasta': #set $ext = 'fasta' #else: - #if $single_or_paired.input_mate1.is_of_type('fastq.gz'): + #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"): #set compressed = 'GZ' - #else if $single_or_paired.input_mate1.is_of_type('fastq.bz2'): + #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"): #set compressed = 'BZ2' #end if #set $ext = 'fastq' #end if ln -s $single_or_paired.input_mate1 ./mate1.$ext && ln -s $single_or_paired.input_mate2 ./mate2.$ext && + #else if $single_or_paired.single_or_paired_opts == 'paired_collection': + #if $single_or_paired.input_1.forward.ext == 'fasta': + #set $ext = 'fasta' + #else: + #if $single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"): + #set compressed = 'GZ' + #else if $single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set compressed = 'BZ2' + #end if + #set $ext = 'fastq' + #end if + ln -s ${single_or_paired.input_1.forward} ./mate1.$ext && + ln -s ${single_or_paired.input_1.reverse} ./mate2.$ext && + #else if $single_or_paired.single_or_paired_opts == 'paired_interleaved': + #if $single_or_paired.input_1.ext == 'fasta': + #set $ext = 'fasta' + #else: + #if $single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"): + #set compressed = 'GZ' + #else if $single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"): + #set compressed = 'BZ2' + #end if + #set $ext = 'fastq' + #end if + ln -s $single_or_paired.input_1 ./mate1.$ext && #end if #if $geneMap: ln -s "$geneMap" ./geneMap.${geneMap.ext} && @@ -82,22 +115,32 @@ #if $single_or_paired.single_or_paired_opts == 'single': --libType ${single_or_paired.strandedness} #if $compressed == 'GZ': - --unmatedReads <(zcat ./single.$ext) + --unmatedReads <(zcat < ./single.$ext) #else if $compressed == 'BZ2': - --unmatedReads <(bzcat ./single.$ext) + --unmatedReads <(bzcat < ./single.$ext) #else: --unmatedReads ./single.$ext #end if #else: - #if $compressed == 'GZ': - --mates1 <(zcat ./mate1.$ext) - --mates2 <(zcat ./mate2.$ext) - #else if $compressed == 'BZ2': - --mates1 <(bzcat ./mate1.$ext) - --mates2 <(bzcat ./mate2.$ext) + #if $single_or_paired.single_or_paired_opts == 'paired_interleaved': + #if $compressed == 'BZ2': + --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1) + --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2) + #else: + --mates1 <(seqtk seq -1 ./mate1.$ext) + --mates2 <(seqtk seq -2 ./mate1.$ext) + #end if #else: - --mates1 ./mate1.$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.$ext + #end if #end if --libType "${single_or_paired.orientation}${single_or_paired.strandedness}" #end if @@ -113,9 +156,7 @@ --incompatPrior $adv.incompatPrior $adv.consistentHits $adv.dumpEq - #if str($adv.gcSizeSamp): - --gcSizeSamp $adv.gcSizeSamp - #end if + $adv.reduceGCMemory #if str($adv.biasSpeedSamp): --biasSpeedSamp $adv.biasSpeedSamp #end if @@ -195,21 +236,29 @@ + + - + - - - - - - - + + + + + + + + + + + + + @@ -247,8 +296,9 @@ help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" /> - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -421,6 +535,43 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +