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comparison dr-disco_detect.xml @ 3:5348cfd3ba5c draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit b6ccc6d8a9a9061207040561b494b7cf2ee3f885
author erasmus-medical-center
date Thu, 10 Aug 2017 05:38:27 -0400
parents 173ca9768e22
children d58d99a070ce
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2:173ca9768e22 3:5348cfd3ba5c
1 <tool id="dr_disco_intronic" name="Dr. Disco (intronic)" version="@TOOL_VERSION@-g0"> 1 <tool id="dr_disco_detect" name="Dr. Disco (detect)" version="@TOOL_VERSION@-g0">
2 <description>Detects break-points in RNA-seq</description> 2 <description>Detects break-points in RNA-seq</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 6
9 9
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 dr-disco 11 dr-disco
12 detect 12 detect
13 --min-e-score '${min_e_score}' 13 --min-e-score '${min_e_score}'
14 '${table_fusion_events}'
15 '${star_discordant_alignment_fixed}' 14 '${star_discordant_alignment_fixed}'
15 '${output_fusion_events}'
16 ]]></command> 16 ]]></command>
17 <inputs> 17 <inputs>
18 <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" /> 18 <param name="star_discordant_alignment_fixed" type="data" format="bam" label="Discordant alignment file of STAR (processed with dr-disco fix)" />
19 <param name="min_e_score" argument="--min-e-score" type="integer" value="8" min="0" 19 <param name="min_e_score" argument="--min-e-score" type="integer" value="8" min="0"
20 label="Minimal score to initiate pulling sub-graphs" help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." /> 20 label="Minimal score to initiate pulling sub-graphs" help="Larger numbers boost performance but result in suboptimal results. Values of 8 and below are considered to be very safe (this corresponds to initiate merging already from clusters that consist of 2 or 3 reads)." />
21 </inputs> 21 </inputs>
22 22
23 <outputs> 23 <outputs>
24 <data name="table_fusion_events" format="tabular" label="${tool.name} on ${$star_discordant_alignment_fixed.name}" /> 24 <data name="output_fusion_events" format="tabular" label="${tool.name} on ${star_discordant_alignment_fixed.name}" />
25 </outputs> 25 </outputs>
26 26
27 <tests> 27 <tests>
28 <test> 28 <test>
29 <param name="star_discordant_alignment_fixed" value="detect.bam" /> 29 <param name="star_discordant_alignment_fixed" value="detect.bam" />
30 <param name="min_e_score" value="8" /> 30 <param name="min_e_score" value="8" />
31 31
32 <output name="table_fusion_events" file="detect.txt" /> 32 <output name="output_fusion_events" file="detect.txt" />
33 </test> 33 </test>
34 </tests> 34 </tests>
35 35
36 <help><![CDATA[ 36 <help><![CDATA[
37 37