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comparison tophat_fusion_post.xml @ 1:75845643f9dd

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Requirement fixes and fixed sample loc file."
author devteam@galaxyproject.org
date Mon, 27 Jan 2014 14:30:21 -0500
parents 70f710e91120
children 2f75d0317ee5
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0:70f710e91120 1:75845643f9dd
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">tophat2</requirement> 5 <requirement type="package" version="2.2.28">blast+</requirement>
6 <requirement type="package" version="2.1.0">bowtie2</requirement>
6 </requirements> 7 </requirements>
7 <command> 8 <command>
8 ## Set up tophat_out structure. 9 ## 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 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
10 11
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 --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 #if str($is_human) == 'No':
24 --non-human 25 --non-human
25 #end if 26 #end if
26 27
27 ## Bowtie2 indices. 28 ## Bowtie2 indices.
28 ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} 29 ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
29 </command> 30 </command>
30 31
31 <inputs> 32 <inputs>
32 <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=""/>
33 <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=""/>