Mercurial > repos > jjohnson > gmap
diff gsnap.xml @ 8:a89fec682254
gmap/gsnap updated to version 2011-11-30
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Thu, 08 Dec 2011 11:00:46 -0600 |
parents | 561503a442f0 |
children |
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--- a/gsnap.xml Tue Nov 08 13:26:41 2011 -0600 +++ b/gsnap.xml Thu Dec 08 11:00:46 2011 -0600 @@ -1,12 +1,7 @@ -<tool id="gsnap" name="GSNAP" version="2.0.0"> +<tool id="gsnap" name="GSNAP" version="2.0.1"> <description>Genomic Short-read Nucleotide Alignment Program</description> <requirements> <requirement type="binary">gsnap</requirement> - <!-- proposed tag for added datatype dependencies --> - <requirement type="datatype">gmapdb</requirement> - <requirement type="datatype">gmapsnpindex</requirement> - <requirement type="datatype">splicesites.iit</requirement> - <requirement type="datatype">introns.iit</requirement> </requirements> <version_string>gsnap --version</version_string> <command> @@ -25,10 +20,16 @@ #if $refGenomeSource.use_splicing.src == 'gmapdb': #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: -s $refGenomeSource.use_splicing.splicemap.value + #if $computation.trim_mismatch_score.__str__ == '0': + $ambig_splice_noclip + #end if #end if #elif $refGenomeSource.use_splicing.src == 'history': #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0: -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap) + #if $computation.trim_mismatch_score.__str__ == '0': + $ambig_splice_noclip + #end if #end if #end if #if $refGenomeSource.use_snps.src == 'gmapdb': @@ -43,9 +44,11 @@ #if $refGenomeSource.mode.__str__ != '': --mode=$refGenomeSource.mode #end if + #* ## No longer in options as of version 2011-11-30 #if $mapq_unique_score.__str__ != '': --mapq-unique-score=$mapq_unique_score #end if + *# #if $computation.options == "advanced": #if $computation.max_mismatches.__str__ != '': --max-mismatches=$computation.max_mismatches @@ -82,6 +85,9 @@ #if $computation.trim_mismatch_score.__str__ != '': --trim-mismatch-score=$computation.trim_mismatch_score #end if + #if $computation.trim_indel_score.__str__ != '': + --trim-indel-score=$computation.trim_indel_score + #end if ## TODO - do we need these options (Is it tally XOR runlength?): ## --tallydir= --use-tally=tally ## --runlengthdir --use-runlength=runlength @@ -206,6 +212,12 @@ #if $seq.paired.pairmax_rna.__str__ != '': --pairmax-rna=$seq.paired.pairmax_rna #end if + #if $seq.paired.pairexpect.__str__ != '': + --pairexpect=$seq.paired.pairexpect + #end if + #if $seq.paired.pairdev.__str__ != '': + --pairdev=$seq.paired.pairdev + #end if $seq.fastq $seq.paired.fastq #else $seq.fastq @@ -245,7 +257,11 @@ <option value="FF">fwd-fwd, same strand</option> </param> <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."/> - <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."/> + <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."/> + <param name="pairexpect" type="integer" value="" optional="true" label="Expected paired-end length" + help="Used for calling splices in medial part of paired-end reads (default 200)"/> + <param name="pairdev" type="integer" value="" optional="true" label="Allowable deviation from expected paired-end length" + help="Used for calling splices in medial part of paired-end reads (default 25)"/> </when> </conditional> <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" /> @@ -281,9 +297,11 @@ </when> </conditional> + <!-- No longer in options as of version 2011-11-30 <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold" help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this (if not selected, then reports all multiple results, up to npaths)" /> + --> <!-- GMAPDB for alignment --> <conditional name="refGenomeSource"> @@ -405,6 +423,9 @@ <when value="history"> <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map" help="built with GMAP IIT"/> + <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites" + help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. + This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/> </when> <when value="gmapdb"> <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help=""> @@ -412,6 +433,9 @@ <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/> </options> </param> + <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites" + help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron. + This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/> </when> </conditional> @@ -457,8 +481,12 @@ </param> <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"/> <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"/> - <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 3)" - 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." /> + <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 2)" + 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 + 1-mismatch alignment, it will not try to find a terminal alignment. + Note that this default value may not be low enough if you want to + obtain terminal alignments for very short reads, although such reads + probably don't have enough specificity for terminal alignments anyway." /> <param name="indel_penalty" type="integer" value="" optional="true" label="Penalty for an indel (default 2)" 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" /> <param name="indel_endlength" type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" /> @@ -474,7 +502,9 @@ <option value="off">off</option> </param> <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)" - help="to turn off trimming, specify 0"/> + help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/> + <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)" + help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/> <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" help="generated by gsnap_tally and iit_store"/>