Mercurial > repos > trinity_ctat > ctat_gmap_fusion
comparison ctat_gmap_fusion.xml @ 0:966ea55e1aae draft default tip
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| author | trinity_ctat |
|---|---|
| date | Tue, 17 Jul 2018 11:52:28 -0400 |
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| -1:000000000000 | 0:966ea55e1aae |
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| 1 <tool id="ctat_gmap_fusion" name="ctat_gmap_fusion" version="1.0.0" profile="17.05"> | |
| 2 <description>Fusion-finding Using De novo RNA-Seq Transcript Assemblies</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.4.0">gmap-fusion</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="default"> | |
| 7 GMAP-fusion | |
| 8 -T $assembled_trans | |
| 9 --left_fq $left_input | |
| 10 --right_fq $right_input | |
| 11 --genome_lib_dir "${genome_resource_lib.fields.path}" | |
| 12 --output "subdir" | |
| 13 </command> | |
| 14 <stdio> | |
| 15 <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> | |
| 16 </stdio> | |
| 17 <regex match="Must investigate error above." | |
| 18 source="stderr" | |
| 19 level="fatal" | |
| 20 description="Unknown error encountered" /> | |
| 21 <inputs> | |
| 22 <param format="fasta" name="assembled_trans" type="data" label="Assembled Transcripts (ie. Trinity or DISCASM output)" help="Trinity or DISCASM generated transcript fasta"/> | |
| 23 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/> | |
| 24 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/> | |
| 25 <param name="genome_resource_lib" type="select" label="Select a reference genome"> | |
| 26 <options from_data_table="ctat_genome_resource_libs"> | |
| 27 <filter type="sort_by" column="2" /> | |
| 28 <validator type="no_options" message="No indexes are available" /> | |
| 29 </options> | |
| 30 </param> | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data format="tabular" name="gmapfusion_candidates" label="${tool.name} on ${on_string}: GMAP-fusion candidates" from_work_dir="subdir/GMAP-fusion.final"/> | |
| 34 </outputs> | |
| 35 | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name="left_input" value="GMAP/reads_1.fq.gz" /> | |
| 39 <param name="right_input" value="GMAP/reads_2.fq.gz" /> | |
| 40 <param name="assembled_trans" value="GMAP/transcripts.fa" /> | |
| 41 <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing? | |
| 42 <param name="genome_resource_lib.fields.path" value="?????" /> | |
| 43 --> | |
| 44 <output name="gmapfusion_candidates" file="GMAP/fusion.reads_1_2.final" /> | |
| 45 </test> | |
| 46 </tests> | |
| 47 | |
| 48 <help> | |
| 49 .. class:: infomark | |
| 50 | |
| 51 GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly. Please read more here_. | |
| 52 | |
| 53 .. _here: https://github.com/GMAP-fusion/GMAP-fusion/wiki | |
| 54 </help> | |
| 55 </tool> |