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comparison tophat_fusion_post.xml @ 3:2f75d0317ee5

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Use Bowtie rather than Bowtie2 and update wrapper to fix Cheetah syntax bug.
author devteam@galaxyproject.org
date Mon, 10 Feb 2014 12:13:22 -0500
parents 75845643f9dd
children 51ede4e7d4f0
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2:664f7d964231 3:2f75d0317ee5
1 <tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1"> 1 <tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1">
2 <description>post-processing to identify fusion genes</description> 2 <description>post-processing to identify fusion genes</description>
3 <version_command>tophat-fusion-post --version</version_command> 3 <version_command>tophat-fusion-post --version</version_command>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.2.28">blast+</requirement> 5 <requirement type="package" version="2.2.28">blast+</requirement>
6 <requirement type="package" version="2.1.0">bowtie2</requirement> 6 <requirement type='package' version="0.12.7">bowtie</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 ## Set up tophat_out structure. 9 ## Set up tophat_out structure.
10 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out; 10 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
11 11
12 ## Set up blast directory structure. 12 ## Set up blast directory structure.
13 #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} 13 #set blast_db_path = $__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')
14 ln -s ${blast_db_path}/ blast; 14 ln -s ${blast_db_path}/ blast;
15 15
16 ## Set up additional files: 16 ## Set up additional files:
17 ln -s ${blast_db_path}/refGene.txt .; 17 ln -s ${blast_db_path}/refGene.txt .;
18 ln -s ${blast_db_path}/ensGene.txt .; 18 ln -s ${blast_db_path}/ensGene.txt .;
23 --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 --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 $fusion_multireads
24 #if str($is_human) == 'No': 24 #if str($is_human) == 'No':
25 --non-human 25 --non-human
26 #end if 26 #end if
27 27
28 ## Bowtie2 indices. 28 ## Bowtie indices.
29 ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} 29 ${__get_data_table_entry__('bowtie_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
30 </command> 30 </command>
31 31
32 <inputs> 32 <inputs>
33 <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/> 33 <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/>
34 <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/> 34 <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/>