Mercurial > repos > devteam > tophat_fusion_post
comparison tophat_fusion_post.xml @ 1:75845643f9dd
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=""/> |