[galaxy-commits] commit/galaxy-central: 3 new changesets

17 Dec 2013

3 new commits in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/08320798463e/
Changeset:   08320798463e
User:        nsoranzo
Date:        2013-12-06 11:17:25
Summary:     Specify mosaik v. 1.1.0021 (last compatible with the wrapper). Add requirement for samtools.
Affected #:  1 file

diff -r a29d54619813d5da992b897557162a360b8d610c -r 08320798463e173f61f0b53fbd2db43419d373e2 tools/sr_mapping/mosaik.xml

--- a/tools/sr_mapping/mosaik.xml
+++ b/tools/sr_mapping/mosaik.xml
@@ -1,7 +1,10 @@
 <?xml version="1.0"?><tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"><description/>
-  <requirements><requirement type="package">mosaik</requirement></requirements>
+  <requirements>
+    <requirement type="package" version="1.1.0021">mosaik</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements><command>
     #set $processors = '-p ${GALAXY_SLOTS:-4}'
     #set $lm = ''


https://bitbucket.org/galaxy/galaxy-central/commits/5fbc02eff708/
Changeset:   5fbc02eff708
User:        nsoranzo
Date:        2013-12-06 11:20:56
Summary:     Fix for failure preparing job: "NotFound: cannot find 'mfl'" with paired-end library.

Add mate FASTQ file to inputs.
'ls' param was not used.
Add missing '-mfl ' to MosaikBuild command.
Remove always empty $lm variable.
Add <version_command>.
Affected #:  1 file

diff -r 08320798463e173f61f0b53fbd2db43419d373e2 -r 5fbc02eff708cc86afd60a4fa7588c9f72e877b5 tools/sr_mapping/mosaik.xml
--- a/tools/sr_mapping/mosaik.xml
+++ b/tools/sr_mapping/mosaik.xml
@@ -1,28 +1,30 @@
 <?xml version="1.0"?>
-<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1">
+<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.2"><description/><requirements><requirement type="package" version="1.1.0021">mosaik</requirement><requirement type="package" version="0.1.18">samtools</requirement></requirements>
+  <version_command>MosaikAligner | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | grep -o 'MosaikAligner [[:digit:].]\{1,\}'</version_command><command>
     #set $processors = '-p ${GALAXY_SLOTS:-4}'
-    #set $lm = ''
-    #if $paired.kind == 'single':
-        #set $mfl = ''
-        #set $ls  = ''
-    #else:
-        #set $ls = '-ls $mfl'
-    #end if
     MosaikBuild -fr
     #if $genomeSource.refGenomeSource == 'indexed':
         ${genomeSource.indexReference.fields.path}
     #else:
-        $genomeSource.historyReference
+        ${genomeSource.historyReference}
     #end if
-        -oa mosaik_ref_file;
-    MosaikBuild  -q $reads $mfl -st $st -out mosaik_reads_file;
-    MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15;
+    -oa mosaik_ref_file;
+    MosaikBuild -q $reads
+    #if $paired.kind == 'single'
+      #set $ls_string  = ''
+    #else
+        -q2 ${paired.reads2}
+        -mfl ${paired.mfl}
+        #set $ls_string = '-ls %s' % $paired.ls
+    #end if
+    -st $st -out mosaik_reads_file;
+    MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls_string -mm $mm -mhp $mhp -act $act -bw $bw $processors -hs 15;
     MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file;
     #if str($outFormat) == 'bam':
         samtools sort sam_bam_file sorted_bam;
@@ -50,12 +52,12 @@
         <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/></when></conditional>
-    <param format="fastq" name="reads" type="data" label="Fastq Reads File"/>
-    <param name="outFormat" type="select" label="Output Format">
-      <option value="sam">Sam</option>
-      <option value="bam">Bam</option>
+    <param format="fastq" name="reads" type="data" label="FASTQ reads file" />
+    <param name="outFormat" type="select" label="Output format">
+      <option value="sam">SAM</option>
+      <option value="bam">BAM</option></param>
-    <param name="st" type="select" label="Sequencing Technology Used">
+    <param name="st" type="select" label="Sequencing technology used"><option value="454">454</option><option value="illumina">Illumina</option><option value="solid">Solid</option>
@@ -69,14 +71,15 @@
       </param><when value="single"/><when value="paired">
-        <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/>
-        <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/>
+        <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" />
+        <param name="mfl" type="integer" value="200" label="Median fragment length" />
+        <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" /></when></conditional>
-    <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/>
-    <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/>
-    <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/>
-    <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/>
+    <param name="mm" type="integer" value="6" label="Number of mismatches allowed per sequence" />
+    <param name="act" type="integer" value="35" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" />
+    <param name="bw" type="integer" value="9" label="Smith-Waterman band width" />
+    <param name="mhp" type="integer" value="100" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" /></inputs><outputs><data format="sam" name="output">


https://bitbucket.org/galaxy/galaxy-central/commits/97c69fcfeaac/
Changeset:   97c69fcfeaac
User:        dannon
Date:        2013-12-17 15:00:44
Summary:     Merged in nsoranzo/galaxy-central (pull request #271)

Fixes for MOSAIK tool
Affected #:  1 file

diff -r 3eb13c85bf4140448865328b9c6feaed96d8682f -r 97c69fcfeaac1756a7ad5d92c8ade74b2d611561 tools/sr_mapping/mosaik.xml
--- a/tools/sr_mapping/mosaik.xml
+++ b/tools/sr_mapping/mosaik.xml
@@ -1,25 +1,30 @@
 <?xml version="1.0"?>
-<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1">
+<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.2"><description/>
-  <requirements><requirement type="package">mosaik</requirement></requirements>
+  <requirements>
+    <requirement type="package" version="1.1.0021">mosaik</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <version_command>MosaikAligner | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | grep -o 'MosaikAligner [[:digit:].]\{1,\}'</version_command><command>
     #set $processors = '-p ${GALAXY_SLOTS:-4}'
-    #set $lm = ''
-    #if $paired.kind == 'single':
-        #set $mfl = ''
-        #set $ls  = ''
-    #else:
-        #set $ls = '-ls $mfl'
-    #end if
     MosaikBuild -fr
     #if $genomeSource.refGenomeSource == 'indexed':
         ${genomeSource.indexReference.fields.path}
     #else:
-        $genomeSource.historyReference
+        ${genomeSource.historyReference}
     #end if
-        -oa mosaik_ref_file;
-    MosaikBuild  -q $reads $mfl -st $st -out mosaik_reads_file;
-    MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15;
+    -oa mosaik_ref_file;
+    MosaikBuild -q $reads
+    #if $paired.kind == 'single'
+      #set $ls_string  = ''
+    #else
+        -q2 ${paired.reads2}
+        -mfl ${paired.mfl}
+        #set $ls_string = '-ls %s' % $paired.ls
+    #end if
+    -st $st -out mosaik_reads_file;
+    MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls_string -mm $mm -mhp $mhp -act $act -bw $bw $processors -hs 15;
     MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file;
     #if str($outFormat) == 'bam':
         samtools sort sam_bam_file sorted_bam;
@@ -47,12 +52,12 @@
         <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/></when></conditional>
-    <param format="fastq" name="reads" type="data" label="Fastq Reads File"/>
-    <param name="outFormat" type="select" label="Output Format">
-      <option value="sam">Sam</option>
-      <option value="bam">Bam</option>
+    <param format="fastq" name="reads" type="data" label="FASTQ reads file" />
+    <param name="outFormat" type="select" label="Output format">
+      <option value="sam">SAM</option>
+      <option value="bam">BAM</option></param>
-    <param name="st" type="select" label="Sequencing Technology Used">
+    <param name="st" type="select" label="Sequencing technology used"><option value="454">454</option><option value="illumina">Illumina</option><option value="solid">Solid</option>
@@ -66,14 +71,15 @@
       </param><when value="single"/><when value="paired">
-        <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/>
-        <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/>
+        <param format="fastq" name="reads2" type="data" label="FASTQ 2nd mate" />
+        <param name="mfl" type="integer" value="200" label="Median fragment length" />
+        <param name="ls" type="integer" min="0" value="50" label="Local alignment search radius to rescue mates" help="A large value slows down performances" /></when></conditional>
-    <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/>
-    <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/>
-    <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/>
-    <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/>
+    <param name="mm" type="integer" value="6" label="Number of mismatches allowed per sequence" />
+    <param name="act" type="integer" value="35" label="Alignment candidate threshold" help="Determines which hash regions will be aligned with Smith-Waterman" />
+    <param name="bw" type="integer" value="9" label="Smith-Waterman band width" />
+    <param name="mhp" type="integer" value="100" label="Maximum number of positions stored per seed" help="Number of places in the reference the aligner will try to place a particular hash" /></inputs><outputs><data format="sam" name="output">

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: 3 new changesets

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