# 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 @@
+
+
-
+
-
-
-
-
-
-
-
+
+
+
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+
+
+
+
+
+
+
+
+
@@ -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" />
-
+
+
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+
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+
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@@ -421,6 +535,43 @@
+
+
+
+
+
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+