Mercurial > repos > rnateam > segemehl
changeset 7:be1a3cc2cf45 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit b193689f9f30ce65a77be2d2c00929e3335a7d82
author | bgruening |
---|---|
date | Wed, 26 Jul 2017 15:25:28 -0400 |
parents | c6cef240817e |
children | 338ecc1500e4 |
files | segemehl.xml test-data/testmap2.sam |
diffstat | 2 files changed, 27 insertions(+), 9 deletions(-) [+] |
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--- a/segemehl.xml Wed Jul 26 10:14:42 2017 -0400 +++ b/segemehl.xml Wed Jul 26 15:25:28 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="segemehl" name="segemehl" version="0.2.0.2"> +<tool id="segemehl" name="segemehl" version="0.2.0.3"> <description>short read mapping with gaps</description> <requirements> <requirement type="package" version="0.2.0">segemehl</requirement> @@ -72,12 +72,12 @@ #if $maxout: --maxout $maxout #end if - #if str( $splitreads.splits ) == "--split": + #if str( $splitreads.splits ) == "splits": --splits - --minsplicecover $minsplicecover - --minfragscore $minfragscore - --minfraglen $minfraglen - --splicescorescale $splicescorescale + --minsplicecover $splitreads.minsplicecover + --minfragscore $splitreads.minfragscore + --minfraglen $splitreads.minfraglen + --splicescorescale $splitreads.splicescorescale #end if -M $maxinterval -E $evalue @@ -131,9 +131,9 @@ <conditional name="splitreads"> <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)"> <option value="nosplit">No splits</option> - <option value="--splits">Split reads</option> + <option value="splits">Split reads</option> </param> - <when value="--splits"> + <when value="splits"> <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" /> <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" /> <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" /> @@ -172,9 +172,18 @@ <param name="own_reference_genome" value="chr1.fa" /> <param name="library" value="single" /> <param name="input_query" value="test.fastq" /> - <param name="splits" value="true" /> + <param name="splits" value="nosplit" /> <output name="segemehl_out" file="testmap.sam" lines_diff="2" /> </test> + <test> + <param name="genomeSource" value="history" /> + <param name="own_reference_genome" value="chr1.fa" /> + <param name="library" value="single" /> + <param name="input_query" value="test.fastq" /> + <param name="splits" value="splits" /> + <param name="minsplicecover" value="40" /> + <output name="segemehl_out" file="testmap2.sam" lines_diff="2" /> + </test> </tests> <help> <![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testmap2.sam Wed Jul 26 15:25:28 2017 -0400 @@ -0,0 +1,9 @@ +@HD VN:1.0 +@SQ SN:TestChromosomeForGalaxy LN:3459 +@PG ID:segemehl VN:0.2.0-$Rev: 418 $ ($Date: 2015-01-05 05:17:35 -0500 (Mon, 05 Jan 2015) $) CL:segemehl.x -t 2 -d test-data/chr1.fa -i test-data/chr1.idx -q test-data/test.fastq -m 12 -A 85 -H 1 -M 100 -E 5.0 -D 1 -s --splits --minsplicecover 40 -o testout2.sam +10.516 HWI-EAS100R:1:1:550:1622/1 0 TestChromosomeForGalaxy 182 255 70M * 0 0 CATGTACTGTTAAAGCGTGCGTTTATTTCAAACATTAATGAAATTTGCAGAACCCAAACTAAAGAGAGAG 3MIa!,$)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