| Previous changeset 7:561503a442f0 (2011-11-08) Next changeset 9:7f032685214b (2011-12-08) |
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Commit message:
gmap/gsnap updated to version 2011-11-30 |
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modified:
gmap.xml gmap_build.xml gsnap.xml iit_store.xml snpindex.xml |
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| diff -r 561503a442f0 -r a89fec682254 gmap.xml --- a/gmap.xml Tue Nov 08 13:26:41 2011 -0600 +++ b/gmap.xml Thu Dec 08 11:00:46 2011 -0600 |
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| b'@@ -1,13 +1,7 @@\n-<tool id="gmap" name="GMAP" version="2.0.0">\n+<tool id="gmap" name="GMAP" version="2.0.1">\n <description>Genomic Mapping and Alignment Program for mRNA and EST sequences</description>\n <requirements>\n <requirement type="binary">gmap</requirement>\n- <!-- proposed tag for added datatype dependencies -->\n- <requirement type="datatype">gmapdb</requirement>\n- <requirement type="datatype">gmap_annotation</requirement>\n- <requirement type="datatype">gmap_splicesites</requirement>\n- <requirement type="datatype">gmap_introns</requirement>\n- <requirement type="datatype">gmap_snps</requirement>\n </requirements>\n <version_string>gmap --version</version_string>\n <command>\n@@ -49,9 +43,11 @@\n #elif $result.format == "sam":\n --format=$result.sam_paired_read\n $result.no_sam_headers \n+ #* Removed in gmap version 2011-11-30\n #if len($result.noncanonical_splices.__str__) > 0\n --noncanonical-splices=$result.noncanonical_splices\n #end if\n+ *#\n #if len($result.read_group_id.__str__) > 0\n --read-group-id=$result.read_group_id\n #end if\n@@ -70,35 +66,50 @@\n #if $computation.options == "advanced":\n $computation.nosplicing\n $computation.cross_species\n- --min-intronlength=$computation.min_intronlength\n- --intronlength=$computation.intronlength\n- --localsplicedist=$computation.localsplicedist\n- --totallength=$computation.totallength\n- --trimendexons=$computation.trimendexons\n+ #if len($computation.min_intronlength.__str__) > 0\n+ --min-intronlength=$computation.min_intronlength\n+ #end if\n+ #if len($computation.intronlength.__str__) > 0\n+ --intronlength=$computation.intronlength\n+ #end if\n+ #if len($computation.localsplicedist.__str__) > 0\n+ --localsplicedist=$computation.localsplicedist\n+ #end if\n+ #if len($computation.totallength.__str__) > 0\n+ --totallength=$computation.totallength\n+ #end if\n+ #if len($computation.trimendexons.__str__) > 0\n+ --trimendexons=$computation.trimendexons\n+ #end if\n --direction=$computation.direction\n --canonical-mode=$computation.canonical\n --prunelevel=$computation.prunelevel\n --allow-close-indels=$computation.allow_close_indels\n- --microexon-spliceprob=$computation.microexon_spliceprob\n- #if int($computation.chimera_margin) >= 0:\n+ #if len($computation.microexon_spliceprob.__str__) >= 0:\n+ --microexon-spliceprob=$computation.microexon_spliceprob\n+ #end if\n+ #if len($computation.chimera_margin.__str__) >= 0:\n --chimera-margin=$computation.chimera_margin\n #end if\n #end if\n #if $advanced.options == "used":\n- #if int($advanced.npaths) >= 0:\n+ #if len($advanced.npaths.__str__) > 0:\n --npaths=$advanced.npaths\n #end if\n- #if int($advanced.chimera_overlap) > 0:\n+ #if len($advanced.suboptimal_score.__str__) > 0:\n+ --suboptimal-score=$advanced.suboptimal_score\n+ #end if\n+ #if len($advanced.chimera_overlap.__str__) > 0:\n --chimera_overlap=$advanced.chimera_overlap\n #end if\n $advanced.protein\n $advanced.tolerant\n $advanced.nolengths\n $advanced.invertmode\n- #if int($advanced.introngap) > 0:\n+ #if len($advanced.introngap.__str__) > 0:\n --introngap=$advanced.introngap\n #end if\n- #if int($advanced.wraplength) > 0:\n+ #if len($advanced.wraplength.__str__) > 0:\n --wraplength=$advanced.wraplength\n #end if\n #end if\n@@ -200,11 +211,22 @@\n <when value="default"/>\n <when value="advanced">\n <param name="nosplicing" type="boolean" truevalue="--nosplicing" falsevalue="" checked="false" label="Turn off splicing" help="(useful for aligning genomic sequences onto a genome)"/>\n- <param name="min_intronlength" type="integer" value="9" label="Min length for one internal intron '..b'essage="slice probability between 0.00 and 1.00" min="0" max="1"/> \n </param>\n <param name="prunelevel" type="select" label="Pruning level">\t\n@@ -255,11 +280,24 @@\n <option value="--invertmode=1">Invert cDNA and print genomic (-) strand</option>\n <option value="--invertmode=2">Invert cDNA and print genomic (+) strand</option>\n </param>\n- <param name="introngap" type="integer" value="3" label="Nucleotides to show on each end of intron (default=3)" />\t\n- <param name="wraplength" type="integer" value="50" label="Line Wrap length for alignment (default=50)" />\t\n- <param name="npaths" type="integer" value="-1" optional="true"\n- label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." />\t\n- <param name="chimera_overlap" type="integer" value="0" label="Overlap to show, if any, at chimera breakpoint" />\t\n+ <param name="introngap" type="integer" value="" optional="true" label="Nucleotides to show on each end of intron (default=3)">\t\n+ <validator type="in_range" message="introngap must be positive" min="0" />\n+ </param>\n+ <param name="wraplength" type="integer" value="" optional="true" label="Line Wrap length for alignment (default=50)">\t\n+ <validator type="in_range" message="wraplength must be positive" min="1" />\n+ </param>\n+ <param name="npaths" type="integer" value="" optional="true"\n+ label="Maximum number of paths to show. Ignored if negative. If 0, prints two paths if chimera detected, else one." >\t\n+ <validator type="in_range" message="npaths must be positive" min="0" />\n+ </param>\n+ <param name="suboptimal_score" type="integer" value="" optional="true"\n+ label="Report only paths whose score is within this value of the best path"\n+ help="By default the program prints all paths found." >\t\n+ <validator type="in_range" message="suboptimal_score must be positive" min="0" />\n+ </param>\n+ <param name="chimera_overlap" type="integer" value="" optional="true" label="Overlap to show, if any, at chimera breakpoint (default 0)" >\t\n+ <validator type="in_range" message="chimera_overlap must be positive" min="0" />\n+ </param>\n <param name="tolerant" type="boolean" checked="false" truevalue="--tolerant=true" falsevalue="" \n label="Translates cDNA with corrections for frameshifts"/>\n <param name="protein" type="select" label="Protein alignment" help="">\n@@ -294,10 +332,10 @@\n <option value="coords">coords in table format</option>\n <option value="sam" selected="true">SAM format</option>\n </param>\n- <when value="gmap"/>\n+ <when value="gmap">\n+ </when>\n <when value="summary"/>\n <when value="align">\n-\n </when>\n <when value="continuous">\n </when>\n@@ -320,11 +358,13 @@\n <when value="sam">\n <param name="sam_paired_read" type="boolean" truevalue="sampe" falsevalue="samse" checked="false" label="SAM paired reads"/>\n <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with \'@\'"/>\n+ <!-- Removed in gmap version 2011-11-30\n <param name="noncanonical_splices" type="select" label="Print non-canonical genomic gaps greater than 20 nt in CIGAR string as STRING.">\n <option value="">Use default</option>\n <option value="N">N</option>\n <option value="D">D</option>\n </param>\n+ -->\n <param name="read_group_id" type="text" value="" label="Value to put into read-group id (RG-ID) field"/>\n <param name="read_group_name" type="text" value="" label="Value to put into read-group name (RG-SM) field"/>\n <param name="read_group_library" type="text" value="" label="Value to put into read-group library (RG-LB) field"/>\n' |
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| diff -r 561503a442f0 -r a89fec682254 gmap_build.xml --- a/gmap_build.xml Tue Nov 08 13:26:41 2011 -0600 +++ b/gmap_build.xml Thu Dec 08 11:00:46 2011 -0600 |
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| @@ -2,9 +2,6 @@ <description>a database genome index for GMAP and GSNAP</description> <requirements> <requirement type="binary">gmap_build</requirement> - <!-- proposed tag for added datatype dependencies --> - <requirement type="datatype">gmapdb</requirement> - <requirement type="datatype">gmap_snps</requirement> </requirements> <version_string>gmap --version</version_string> <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command> |
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| diff -r 561503a442f0 -r a89fec682254 gsnap.xml --- a/gsnap.xml Tue Nov 08 13:26:41 2011 -0600 +++ b/gsnap.xml Thu Dec 08 11:00:46 2011 -0600 |
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| b'@@ -1,12 +1,7 @@\n-<tool id="gsnap" name="GSNAP" version="2.0.0">\n+<tool id="gsnap" name="GSNAP" version="2.0.1">\n <description>Genomic Short-read Nucleotide Alignment Program</description>\n <requirements>\n <requirement type="binary">gsnap</requirement>\n- <!-- proposed tag for added datatype dependencies -->\n- <requirement type="datatype">gmapdb</requirement>\n- <requirement type="datatype">gmapsnpindex</requirement>\n- <requirement type="datatype">splicesites.iit</requirement>\n- <requirement type="datatype">introns.iit</requirement>\n </requirements>\n <version_string>gsnap --version</version_string>\n <command>\n@@ -25,10 +20,16 @@\n #if $refGenomeSource.use_splicing.src == \'gmapdb\':\n #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:\n -s $refGenomeSource.use_splicing.splicemap.value\n+ #if $computation.trim_mismatch_score.__str__ == \'0\':\n+ $ambig_splice_noclip\n+ #end if\n #end if\n #elif $refGenomeSource.use_splicing.src == \'history\':\n #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:\n -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap)\n+ #if $computation.trim_mismatch_score.__str__ == \'0\':\n+ $ambig_splice_noclip\n+ #end if\n #end if\n #end if\n #if $refGenomeSource.use_snps.src == \'gmapdb\':\n@@ -43,9 +44,11 @@\n #if $refGenomeSource.mode.__str__ != \'\':\n --mode=$refGenomeSource.mode\n #end if\n+ #* ## No longer in options as of version 2011-11-30\n #if $mapq_unique_score.__str__ != \'\':\n --mapq-unique-score=$mapq_unique_score\n #end if\n+ *#\n #if $computation.options == "advanced":\n #if $computation.max_mismatches.__str__ != \'\':\n --max-mismatches=$computation.max_mismatches\n@@ -82,6 +85,9 @@\n #if $computation.trim_mismatch_score.__str__ != \'\':\n --trim-mismatch-score=$computation.trim_mismatch_score\n #end if\n+ #if $computation.trim_indel_score.__str__ != \'\':\n+ --trim-indel-score=$computation.trim_indel_score\n+ #end if\n ## TODO - do we need these options (Is it tally XOR runlength?):\n ## --tallydir= --use-tally=tally\n ## --runlengthdir --use-runlength=runlength\n@@ -206,6 +212,12 @@\n #if $seq.paired.pairmax_rna.__str__ != \'\':\n --pairmax-rna=$seq.paired.pairmax_rna\n #end if\n+ #if $seq.paired.pairexpect.__str__ != \'\':\n+ --pairexpect=$seq.paired.pairexpect\n+ #end if\n+ #if $seq.paired.pairdev.__str__ != \'\':\n+ --pairdev=$seq.paired.pairdev\n+ #end if\n $seq.fastq $seq.paired.fastq\n #else\n $seq.fastq\n@@ -245,7 +257,11 @@\n <option value="FF">fwd-fwd, same strand</option>\n </param>\n <param name="pairmax_dna" type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/>\n- <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used novelspliceing is specified or a splice file is provided. Should probably match the value for localsplicedist."/>\n+ <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used when novel splicing is specified or a splice file is provided. Should probably match the value for localsplicedist."/>\n+ <param name="pairexpect" type="integer" value="" optional="true" label="Expected paired-end length" \n+ '..b' splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. \n+ This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>\n </when>\n <when value="gmapdb">\n <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help="">\n@@ -412,6 +433,9 @@\n <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/>\n </options>\n </param>\n+ <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"\n+ help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. \n+ This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>\n </when>\n </conditional>\n \n@@ -457,8 +481,12 @@\n </param>\n <param name="query_unk_mismatch" type="boolean" checked="false" truevalue="--query-unk-mismatch=1" falsevalue="" label="Count unknown (N) characters in the query as a mismatch"/>\n <param name="genome_unk_mismatch" type="boolean" checked="true" truevalue="" falsevalue="--genome-unk-mismatch=0" label="Count unknown (N) characters in the genome as a mismatch"/>\n- <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 3)" \n- help="(from one end of the read to the best possible position at the other end). To turn off terminal alignments, set this to a high value." />\n+ <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 2)" \n+ help="(from one end of the read to the best possible position at the other end). For example, if this value is 2, then if GSNAP finds an exact or\n+ 1-mismatch alignment, it will not try to find a terminal alignment.\n+ Note that this default value may not be low enough if you want to\n+ obtain terminal alignments for very short reads, although such reads\n+ probably don\'t have enough specificity for terminal alignments anyway." />\n <param name="indel_penalty" type="integer" value="" optional="true" label="Penalty for an indel (default 2)" \n help="Counts against mismatches allowed. To find indels, make indel-penalty less than or equal to max-mismatches. A value < 2 can lead to false positives at read ends" />\n <param name="indel_endlength" type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" />\n@@ -474,7 +502,9 @@\n <option value="off">off</option>\n </param>\n <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)" \n- help="to turn off trimming, specify 0"/>\n+ help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/>\n+ <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)" \n+ help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/>\n <param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results" \n help="generated by gsnap_tally and iit_store"/>\n \n' |
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| diff -r 561503a442f0 -r a89fec682254 iit_store.xml --- a/iit_store.xml Tue Nov 08 13:26:41 2011 -0600 +++ b/iit_store.xml Thu Dec 08 11:00:46 2011 -0600 |
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| @@ -2,13 +2,6 @@ <description>Create a map store for known genes or SNPs</description> <requirements> <requirement type="binary">iit_store</requirement> - <!-- proposed tag for added datatype dependencies --> - <requirement type="datatype">gmap_annotation</requirement> - <requirement type="datatype">gmap_snps</requirement> - <requirement type="datatype">iit</requirement> - <requirement type="datatype">splicesites.iit</requirement> - <requirement type="datatype">introns.iit</requirement> - <requirement type="datatype">snps.iit</requirement> </requirements> <version_string>iit_store --version</version_string> <command interpreter="command"> /bin/bash $shscript 2> $log </command> |
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| diff -r 561503a442f0 -r a89fec682254 snpindex.xml --- a/snpindex.xml Tue Nov 08 13:26:41 2011 -0600 +++ b/snpindex.xml Thu Dec 08 11:00:46 2011 -0600 |
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| @@ -2,11 +2,6 @@ <description>build index files for known SNPs</description> <requirements> <requirement type="binary">snpindex</requirement> - <!-- proposed tag for added datatype dependencies --> - <requirement type="datatype">gmapsnpindex</requirement> - <requirement type="datatype">gmapdb</requirement> - <requirement type="datatype">gmap_snps</requirement> - <requirement type="datatype">snps.iit</requirement> </requirements> <version_string>snpindex --version</version_string> <command interpreter="command"> /bin/bash $shscript 2>1 1> $output </command> |