Mercurial > repos > devteam > tophat_fusion_post
annotate tophat_fusion_post.xml @ 12:f83394a2c2da draft default tip
Uploaded
| author | devteam |
|---|---|
| date | Thu, 27 Feb 2014 15:05:24 -0500 |
| parents | 08f88205d596 |
| children |
| rev | line source |
|---|---|
| 0 | 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> | |
|
1
75845643f9dd
Requirement fixes and fixed sample loc file."
devteam@galaxyproject.org
parents:
0
diff
changeset
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5 <requirement type="package" version="2.2.28">blast+</requirement> |
| 4 | 6 <requirement type="package" version="0.12.7">bowtie</requirement> |
| 7 <requirement type="package" version="2.0.9">tophat2</requirement> | |
| 0 | 8 </requirements> |
| 9 <command> | |
| 10 ## Set up tophat_out structure. | |
| 11 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out; | |
| 12 | |
| 13 ## Set up blast directory structure. | |
|
3
2f75d0317ee5
Use Bowtie rather than Bowtie2 and update wrapper to fix Cheetah syntax bug.
devteam@galaxyproject.org
parents:
1
diff
changeset
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14 #set blast_db_path = $__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path') |
| 0 | 15 ln -s ${blast_db_path}/ blast; |
| 16 | |
| 17 ## Set up additional files: | |
| 18 ln -s ${blast_db_path}/refGene.txt .; | |
| 19 ln -s ${blast_db_path}/ensGene.txt .; | |
| 20 ln -s ${blast_db_path}/mcl .; | |
| 21 | |
| 22 ## Run tophat-fusion-post | |
| 9 | 23 tophat-fusion-post -p \${GALAXY_SLOTS:-4} |
| 0 | 24 --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 $fusion_multireads |
| 25 #if str($is_human) == 'No': | |
| 26 --non-human | |
| 27 #end if | |
| 28 | |
|
3
2f75d0317ee5
Use Bowtie rather than Bowtie2 and update wrapper to fix Cheetah syntax bug.
devteam@galaxyproject.org
parents:
1
diff
changeset
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29 ## Bowtie indices. |
|
10
33aafd74bb31
Fix bugs: (a) use value rather than dbkey to get bowtie indices and (b) point to correct bowtie table.
devteam@galaxyproject.org
parents:
9
diff
changeset
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30 ${__get_data_table_entry__('bowtie_indexes', 'value', $accepted_hits.dbkey, 'path')} |
| 0 | 31 </command> |
| 32 | |
| 33 <inputs> | |
| 34 <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/> | |
| 35 <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/> | |
| 36 <param name="num_fusion_reads" type="integer" value="3" label="Num Fusion Reads" help="Fusions with at least this many supporting reads will be reported."/> | |
| 37 <param name="num_fusion_pairs" type="integer" value="2" label="Num Fusion Pairs" help="Fusions with at least this many supporting pairs will be reported."/> | |
| 38 <param name="num_fusion_both" type="integer" value="0" label="Num Fusion Reads + Pairs" help="The sum of supporting reads and pairs is at least this number for a fusion to be reported."/> | |
| 39 <param name="fusion_read_mismatches" type="integer" value="2" label="Fusion Read Mismatches" help="Reads support fusions if they map across fusion with at most this many mismatches."/> | |
| 40 <param name="fusion_multireads" type="integer" value="2" label="Reads that map to more than this many places will be ignored." help=""/> | |
| 41 <param name="is_human" type="select" label="Is your data from humans?"> | |
| 42 <option value="Yes" selected="True">Yes</option> | |
| 43 <option value="No">No</option> | |
| 44 </param> | |
| 45 </inputs> | |
| 46 | |
| 47 <stdio> | |
| 48 <regex match=".*" source="both" level="log" description="tool progress"/> | |
| 49 </stdio> | |
| 50 | |
| 51 <outputs> | |
| 7 | 52 <data format="tabular" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/> |
| 0 | 53 <data format="html" name="results_html" label="${tool.name} on ${on_string}: html results" from_work_dir="tophatfusion_out/result.html"/> |
| 54 </outputs> | |
| 11 | 55 |
| 0 | 56 </tool> |