Mercurial > repos > rnateam > segemehl
changeset 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 |
files | segemehl.xml test-data/testmap.sam |
diffstat | 2 files changed, 46 insertions(+), 36 deletions(-) [+] |
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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 ${on_string}"/> @@ -159,7 +171,7 @@ <param name="genomeSource" value="history" /> <param name="own_reference_genome" value="chr1.fa" /> <param name="library" value="single" /> - <param name="input_query" value="test.fastq" /> + <param name="input_query" value="test.fastq" /> <param name="splits" value="true" /> <output name="segemehl_out" file="testmap.sam" lines_diff="2" /> </test>
--- a/test-data/testmap.sam Tue Jul 25 10:07:39 2017 -0400 +++ b/test-data/testmap.sam Wed Jul 26 10:14:42 2017 -0400 @@ -1,9 +1,7 @@ @HD VN:1.0 @SQ SN:TestChromosomeForGalaxy LN:3459 -@PG ID:segemehl VN:0.2.0-$Rev: 418 $ ($Date: 2015-01-05 05:17:35 -0500 (Mon, 05 Jan 2015) $) CL:segemehl.x -i chr1.idx -d chr1.fa -q test.fastq -S -m 12 -A 85 -H 1 --minsplicecover 80 --minfragscore 18 --minfraglen 20 --splicescorescale 1.0 +@PG ID:segemehl VN:0.2.0-$Rev: 418 $ ($Date: 2015-01-05 05:17:35 -0500 (Mon, 05 Jan 2015) $) CL:segemehl.x -t 2 -d test-data/chr1.fa -i test-data/chr1.idx -q test-data/test.fastq -m 12 -A 85 -H 1 -M 100 -E 5.0 -D 1 -s -o testout.sam 10.516 HWI-EAS100R:1:1:550:1622/1 0 TestChromosomeForGalaxy 182 255 70M * 0 0 CATGTACTGTTAAAGCGTGCGTTTATTTCAAACATTAATGAAATTTGCAGAACCCAAACTAAAGAGAGAG 3MIa!,$)8EA)!1>tMJ{:2WrL`s|`gg{]'0+Op!6RxNw;V)XKV#Go5}b!`_V]A?!F>{LM(z NM:i:0 MD:Z:70 NH:i:1 XI:i:0 XA:Z:Q 10.2869 HWI-EAS100R:1:1:1698:585/1 0 TestChromosomeForGalaxy 661 255 70M * 0 0 AACCATGCATAAAAGGGGTTCGCCGTTCTCGGAGAGCCACAGAGCCCGGGCCACAGGCAGCTCCTTGCCA Q-a;@)*!F]Za^4!P*B?&!!No!^76b+X[6eOgr1$3:-Ywg;!Vzj!`=+e>YV|ok_z!D<2+jx NM:i:0 MD:Z:70 NH:i:1 XI:i:0 XA:Z:Q 10.2085 HWI-EAS100R:1:1:32:109/2 0 TestChromosomeForGalaxy 1021 255 70M * 0 0 GGGAATTCACCTCAAGAACATCCAAAGTGTGAAGGTGAAGTCCCCCGGACCCCACTGCGCCCAAACCGAA V:e@~!I\GQ>>]?)-qpe!nVI4IJ+4!wE{YoSsVrr~P;PnY/.!a;~!S"n+J#St-g!lQdGA9; NM:i:0 MD:Z:70 NH:i:1 XI:i:0 XA:Z:Q -10.2869 HWI-EAS100R:1:1:1698:585/2 0 TestChromosomeForGalaxy 1321 255 43M * 0 0 CGACTGGAGCTGTTGGTCAGAAATACTGGCGTCTGCCCCCTAA btOb!D1"=hSm"'G_#I{b!!l#6JQ&iq4A`F%Uug!x!'h NM:i:0 MD:Z:43 NH:i:1 XI:i:0 XL:i:2 XA:Z:Q XX:i:1 XY:i:43 XQ:i:0 XC:Z:TestChromosomeForGalaxy XV:i:2123 XT:i:32 -10.2869 HWI-EAS100R:1:1:1698:585/2 0 TestChromosomeForGalaxy 2123 255 27M * 0 0 TGGCAAATCCAACTGACCAGAAGGAAG 7o<%qCKQEtM)!bP>!."DvsX9T}= NM:i:0 MD:Z:27 NH:i:1 XI:i:0 XL:i:2 XA:Z:Q XX:i:44 XY:i:70 XQ:i:1 XP:Z:TestChromosomeForGalaxy XU:i:1363 XS:i:64 10.516 HWI-EAS100R:1:1:550:1623/1 0 TestChromosomeForGalaxy 182 255 70M * 0 0 CATGTACTGTTAAAGCGTGCGTTTATTTCAAACATTAATGAAATTTGCAGAACCCAAACTAAAGAGAGAG 3MIa!,$)8EA)!1>tMJ{:2WrL`s|`gg{]'0+Op!6RxNw;V)XKV#Go5}b!`_V]A?!F>{LM(z NM:i:0 MD:Z:70 NH:i:1 XI:i:0 XA:Z:Q