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comparison segemehl.xml @ 7:be1a3cc2cf45 draft

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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 90b8941e5115
comparison
equal deleted inserted replaced
6:c6cef240817e 7:be1a3cc2cf45
1 <tool id="segemehl" name="segemehl" version="0.2.0.2"> 1 <tool id="segemehl" name="segemehl" version="0.2.0.3">
2 <description>short read mapping with gaps</description> 2 <description>short read mapping with gaps</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.0">segemehl</requirement> 4 <requirement type="package" version="0.2.0">segemehl</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
70 $hardclip 70 $hardclip
71 $order 71 $order
72 #if $maxout: 72 #if $maxout:
73 --maxout $maxout 73 --maxout $maxout
74 #end if 74 #end if
75 #if str( $splitreads.splits ) == "--split": 75 #if str( $splitreads.splits ) == "splits":
76 --splits 76 --splits
77 --minsplicecover $minsplicecover 77 --minsplicecover $splitreads.minsplicecover
78 --minfragscore $minfragscore 78 --minfragscore $splitreads.minfragscore
79 --minfraglen $minfraglen 79 --minfraglen $splitreads.minfraglen
80 --splicescorescale $splicescorescale 80 --splicescorescale $splitreads.splicescorescale
81 #end if 81 #end if
82 -M $maxinterval 82 -M $maxinterval
83 -E $evalue 83 -E $evalue
84 -D $differences 84 -D $differences
85 -s 85 -s
129 </conditional> 129 </conditional>
130 130
131 <conditional name="splitreads"> 131 <conditional name="splitreads">
132 <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)"> 132 <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)">
133 <option value="nosplit">No splits</option> 133 <option value="nosplit">No splits</option>
134 <option value="--splits">Split reads</option> 134 <option value="splits">Split reads</option>
135 </param> 135 </param>
136 <when value="--splits"> 136 <when value="splits">
137 <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" /> 137 <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" />
138 <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" /> 138 <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" />
139 <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" /> 139 <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" />
140 <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score" 140 <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score"
141 help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" /> 141 help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" />
170 <test> 170 <test>
171 <param name="genomeSource" value="history" /> 171 <param name="genomeSource" value="history" />
172 <param name="own_reference_genome" value="chr1.fa" /> 172 <param name="own_reference_genome" value="chr1.fa" />
173 <param name="library" value="single" /> 173 <param name="library" value="single" />
174 <param name="input_query" value="test.fastq" /> 174 <param name="input_query" value="test.fastq" />
175 <param name="splits" value="true" /> 175 <param name="splits" value="nosplit" />
176 <output name="segemehl_out" file="testmap.sam" lines_diff="2" /> 176 <output name="segemehl_out" file="testmap.sam" lines_diff="2" />
177 </test>
178 <test>
179 <param name="genomeSource" value="history" />
180 <param name="own_reference_genome" value="chr1.fa" />
181 <param name="library" value="single" />
182 <param name="input_query" value="test.fastq" />
183 <param name="splits" value="splits" />
184 <param name="minsplicecover" value="40" />
185 <output name="segemehl_out" file="testmap2.sam" lines_diff="2" />
177 </test> 186 </test>
178 </tests> 187 </tests>
179 <help> 188 <help>
180 <![CDATA[ 189 <![CDATA[
181 190