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comparison stringtie.xml @ 11:52f55ad3dee2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 46636ba3d63d34e9ee30a2e0ee28cca0213628c8
author iuc
date Wed, 25 May 2016 15:04:16 -0400
parents ce5e12ebb972
children f70601406e0e
comparison
equal deleted inserted replaced
10:ce5e12ebb972 11:52f55ad3dee2
2 <description>transcript assembly and quantification</description> 2 <description>transcript assembly and quantification</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.0">stringtie</requirement> 4 <requirement type="package" version="1.1.0">stringtie</requirement>
5 </requirements> 5 </requirements>
6 <command><![CDATA[ 6 <command><![CDATA[
7 stringtie "$input_bam" 7 stringtie "$input_bam"
8 -o "$output_gtf" 8 -o "$output_gtf"
9 -p "\${GALAXY_SLOTS:-1}" 9 -p "\${GALAXY_SLOTS:-1}"
10 #if str($guide.use_guide) == 'yes': 10 #if str($guide.use_guide) == 'yes':
11 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation 11 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
12 #if str($guide.output_ballgown) == '-b': 12 #if str($guide.output_ballgown) == '-b':
13 $guide.output_ballgown `pwd` 13 $guide.output_ballgown `pwd`
14 #end if 14 #end if
15 #end if 15 #end if
16 #if str($option_set.options) == 'advanced': 16 #if str($option_set.options) == 'advanced':
17 -l "$option_set.name_prefix" 17 -l "$option_set.name_prefix"
18 -f "$option_set.fraction" 18 -f "$option_set.fraction"
19 -m "$option_set.min_tlen" 19 -m "$option_set.min_tlen"
20 -a "$option_set.min_anchor_len" 20 -a "$option_set.min_anchor_len"
21 -j "$option_set.min_anchor_cov" 21 -j "$option_set.min_anchor_cov"
22 -c "$option_set.min_bundle_cov" 22 -c "$option_set.min_bundle_cov"
23 -g "$option_set.bdist" 23 -g "$option_set.bdist"
24 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming 24 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
25 #if $option_set.A: 25 #if $option_set.A:
26 -A "$gene_abundance_estimation" 26 -A "$gene_abundance_estimation"
27 #end if 27 #end if
28 #if str($option_set.x).strip() != "": 28 #if str($option_set.x).strip() != "":
29 -x "$option_set.x" 29 -x "$option_set.x"
30 #end if 30 #end if
31 #end if 31 #end if
32 ]]> 32 ]]>
33 </command> 33 </command>
34 <inputs> 34 <inputs>
35 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> 35 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
36 <conditional name="guide"> 36 <conditional name="guide">
192 192
193 193
194 ]]> 194 ]]>
195 </help> 195 </help>
196 <citations> 196 <citations>
197 <citation type="doi">doi:10.1038/nbt.3122</citation> 197 <citation type="doi">10.1038/nbt.3122</citation>
198 </citations> 198 </citations>
199 </tool> 199 </tool>