Mercurial > repos > rnateam > segemehl
diff segemehl.xml @ 6:c6cef240817e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 7956a517bb57425e53822bcf2ea0b2c9a54d06e3
| author | bgruening |
|---|---|
| date | Wed, 26 Jul 2017 10:14:42 -0400 |
| parents | 9ffdddb42700 |
| children | be1a3cc2cf45 |
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--- a/segemehl.xml Tue Jul 25 10:07:39 2017 -0400 +++ b/segemehl.xml Wed Jul 26 10:14:42 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="segemehl" name="segemehl" version="0.2.0.1"> +<tool id="segemehl" name="segemehl" version="0.2.0.2"> <description>short read mapping with gaps</description> <requirements> <requirement type="package" version="0.2.0">segemehl</requirement> @@ -14,10 +14,10 @@ ## prepare segemehl index if no reference genome is supplied #if $refGenomeSource.genomeSource == "history": mkdir ./temp_index/ && - #set $temp_index = './temp_index/temp.idx' + #set $temp_index = './temp_index/temp.idx' segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome && #else: - #set $temp_index = $refGenomeSource.index.fields.index_path + #set $temp_index = $refGenomeSource.index.fields.index_path #end if ## execute segemehl @@ -32,34 +32,33 @@ -d ${refGenomeSource.index.fields.db_path} #end if - -i $temp_index + -i $temp_index ## check for single/pair-end #if str( $library.type ) == "single": - #set $query_list = list() + #set $query_list = list() ## prepare inputs #for $fastq in $library.input_query: $query_list.append('%s' % $fastq ) #end for - -q "#echo ' '.join( $query_list )#" + -q "#echo ' '.join( $query_list )#" #else - ## prepare inputs - - #set $mate1 = list() - #set $mate2 = list() - #for $mate_pair in $library.mate_list: - $mate1.append( str($mate_pair.first_strand_query) ) - $mate2.append( str($mate_pair.second_strand_query) ) - #end for + ## prepare inputs + #set $mate1 = list() + #set $mate2 = list() + #for $mate_pair in $library.mate_list: + $mate1.append( str($mate_pair.first_strand_query) ) + $mate2.append( str($mate_pair.second_strand_query) ) + #end for -q #echo ','.join($mate1) -p #echo ','.join($mate2) -I $library.maxinsertsize #end if - -m $minsize - -A $accuracy - -H $hitstrategy + -m $minsize + -A $accuracy + -H $hitstrategy #if str( $prime5 ).strip(): -P "$prime5" #end if @@ -70,19 +69,21 @@ $autoclip $hardclip $order - $splits #if $maxout: --maxout $maxout #end if - -s - + #if str( $splitreads.splits ) == "--split": + --splits --minsplicecover $minsplicecover --minfragscore $minfragscore --minfraglen $minfraglen --splicescorescale $splicescorescale - - -o '$segemehl_out' - + #end if + -M $maxinterval + -E $evalue + -D $differences + -s + -o '$segemehl_out' ]]> </command> <inputs> @@ -127,18 +128,27 @@ </when> </conditional> - <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" /> - <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" /> - <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" /> - <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score" - help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" /> - + <conditional name="splitreads"> + <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)"> + <option value="nosplit">No splits</option> + <option value="--splits">Split reads</option> + </param> + <when value="--splits"> + <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" /> + <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" /> + <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" /> + <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score" + help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" /> + <param name="sevalue" type="float" min="0" value="50.000000" label="max split evalue" help="(--maxsplitevalue)"/> + </when> + <when value="nosplit"> + </when> + </conditional> + <param name="minsize" type="integer" value="12" min="1" label="Minimum size of queries" help="(-m)" /> - <param name="maxout" type="integer" min="0" value="0" optional="True" label="Maximum number of alignments that will be reported" help="(--maxout)" /> <param name="accuracy" type="integer" value="85" min="1" max="100" label="Min percentage of matches per read in semi-global alignment" help="(-A)" /> - <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)"> <option value="1">report only best scoring hits</option> <option value="0">report all scoring hits</option> @@ -149,7 +159,9 @@ <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/> <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="(-C)"/> <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/> - <param name="splits" type="boolean" truevalue="--splits" falsevalue="" checked="false" label="Detect split/spliced reads" help="(--splits)"/> + <param name="differences" type="integer" min="0" value="1" label="search seeds initially with n differences" help="(--differences)"/> + <param name="evalue" type="float" min="0" value="5.000000" label="max evalue" help="(--evalue)"/> + <param name="maxinterval" type="integer" min="1" value="100" label="maximum width of a suffix array interval, i.e. a query seed will be omitted if it matches more than n times" help="(--maxinterval)"/> </inputs> <outputs> <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/> @@ -159,7 +171,7 @@ <param name="genomeSource" value="history" /> <param name="own_reference_genome" value="chr1.fa" /> <param name="library" value="single" /> - <param name="input_query" value="test.fastq" /> + <param name="input_query" value="test.fastq" /> <param name="splits" value="true" /> <output name="segemehl_out" file="testmap.sam" lines_diff="2" /> </test>