Mercurial > repos > jjohnson > defuse
comparison defuse.xml @ 5:3bd1087db05e draft
Add dependecies for bowtie, blat, and faToTwoBit
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 04 Jan 2013 15:01:19 -0600 |
| parents | 679a5c7b1294 |
| children | 6e30713cefb0 |
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| 4:679a5c7b1294 | 5:3bd1087db05e |
|---|---|
| 1 <tool id="defuse" name="DeFuse" version="1.5"> | 1 <tool id="defuse" name="DeFuse" version="1.5"> |
| 2 <description>identify fusion transcripts</description> | 2 <description>identify fusion transcripts</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.5.0">defuse</requirement> | 4 <requirement type="package" version="0.5.0">defuse</requirement> |
| 5 <requirement type="package">bowtie</requirement> | 5 <requirement type="package" version="0.12.7">bowtie</requirement> |
| 6 <requirement type="package">blat</requirement> | 6 <requirement type="package" version="34x10">blat</requirement> |
| 7 <requirement type="package">fatotwobit</requirement> | 7 <requirement type="package" version="34x10">fatotwobit</requirement> |
| 8 </requirements> | 8 </requirements> |
| 9 <command interpreter="command"> /bin/bash $shscript </command> | 9 <command interpreter="command"> /bin/bash $shscript </command> |
| 10 <inputs> | 10 <inputs> |
| 11 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/> | 11 <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads. (FASTQ interlacer will pair reads and remove the unpaired. FASTQ de-interlacer will separate the result into left and right reads.)"/> |
| 12 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/> | 12 <param name="right_pairendreads" type="data" format="fastq" label="right part of read pairs" help="In the same order as the left reads"/> |