forked from NCIP/Trinity_CTAT_galaxy
-
Notifications
You must be signed in to change notification settings - Fork 1
/
gmap_fusion.xml
37 lines (35 loc) · 1.73 KB
/
gmap_fusion.xml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
<tool id="gmap-fusion" name="GMAP-fusion" version="0.0.1">
<description>Fusion-finding Using De novo RNA-Seq Transcript Assemblies</description>
<requirements>
<requirement type="set_environment">FUSION_RESOURCES</requirement>
<requirement type="set_environment">TRINTOOLS</requirement>
</requirements>
<command>
\$TRINTOOLS/GMAP-fusion_v0.0.1/GMAP-fusion
-T $assembled_trans
--left_fq $left_input
--right_fq $right_input
--genome_lib_dir \$FUSION_RESOURCES
--output "subdir"
</command>
<stdio>
<exit_code range="1:" level="fatal" description="Error returned from pipeline" />
</stdio>
<regex match="Must investigate error above."
source="stderr"
level="fatal"
description="Unknown error encountered" />
<inputs>
<param format="fasta" name="assembled_trans" type="data" label="Assembled Transcripts (ie. Trinity or DISCASM output)" help="Trinity or DISCASM generated transcript fasta"/>
<param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
<param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
</inputs>
<outputs>
<data format="tabular" name="gmapfusion_candidates" label="${tool.name} on ${on_string}: GMAP-fusion candidates" from_work_dir="subdir/GMAP-fusion.final"/>
</outputs>
<help>
.. class:: infomark
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_.
.. _here: https://github.com/GMAP-fusion/GMAP-fusion/wiki
</help>
</tool>