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comparison tophat_fusion_post.xml @ 0:70f710e91120

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Initial upload
author devteam@galaxyproject.org
date Mon, 27 Jan 2014 13:16:59 -0500
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children 75845643f9dd
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-1:000000000000 0:70f710e91120
1 <tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1">
2 <description>post-processing to identify fusion genes</description>
3 <version_command>tophat-fusion-post --version</version_command>
4 <requirements>
5 <requirement type="package">tophat2</requirement>
6 </requirements>
7 <command>
8 ## Set up tophat_out structure.
9 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
10
11 ## Set up blast directory structure.
12 #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
13 ln -s ${blast_db_path}/ blast;
14
15 ## Set up additional files:
16 ln -s ${blast_db_path}/refGene.txt .;
17 ln -s ${blast_db_path}/ensGene.txt .;
18 ln -s ${blast_db_path}/mcl .;
19
20 ## Run tophat-fusion-post
21 tophat-fusion-post -p 22
22 --num-fusion-reads $num_fusion_reads --num-fusion-pairs $num_fusion_pairs --num-fusion-both $num_fusion_both --fusion-read-mismatches $fusion_read_mismatches --fusion-multireads $fusion_multireads
23 #if str($is_human) == 'No':
24 --non-human
25 #end if
26
27 ## Bowtie2 indices.
28 ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
29 </command>
30
31 <inputs>
32 <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/>
33 <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/>
34 <param name="num_fusion_reads" type="integer" value="3" label="Num Fusion Reads" help="Fusions with at least this many supporting reads will be reported."/>
35 <param name="num_fusion_pairs" type="integer" value="2" label="Num Fusion Pairs" help="Fusions with at least this many supporting pairs will be reported."/>
36 <param name="num_fusion_both" type="integer" value="0" label="Num Fusion Reads + Pairs" help="The sum of supporting reads and pairs is at least this number for a fusion to be reported."/>
37 <param name="fusion_read_mismatches" type="integer" value="2" label="Fusion Read Mismatches" help="Reads support fusions if they map across fusion with at most this many mismatches."/>
38 <param name="fusion_multireads" type="integer" value="2" label="Reads that map to more than this many places will be ignored." help=""/>
39 <param name="is_human" type="select" label="Is your data from humans?">
40 <option value="Yes" selected="True">Yes</option>
41 <option value="No">No</option>
42 </param>
43 </inputs>
44
45 <stdio>
46 <regex match=".*" source="both" level="log" description="tool progress"/>
47 </stdio>
48
49 <outputs>
50 <data format="txt" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
51 <data format="html" name="results_html" label="${tool.name} on ${on_string}: html results" from_work_dir="tophatfusion_out/result.html"/>
52 </outputs>
53 </tool>