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comparison discasm.xml @ 0:e12b5e204a21 draft

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Adding discasm tool.
author trinity_ctat
date Mon, 30 Oct 2017 11:22:42 -0400
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children e22310df6e56
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1 <tool id="discasm" name="DISCASM" version="1.0.0" profile="17.05">
2 <description>Discordant and Unmapped Read De novo Transcriptome Assembly</description>
3 <requirements>
4 <!-- Added following requirement, but it does not exist in conda yet. -->
5 <requirement type="package" version="1.1.2">discasm</requirement>
6 </requirements>
7 <!--
8 <requirement type="set_environment">TRINTOOLS</requirement>
9 echo $TRINTOOLS
10 /N/dc2/projects/galaxyshared/trinity/third_party_applications
11 But this is only on github. Looks like we need to create a conda package for this one.
12 -->
13 <command detect_errors="default">
14 DISCASM
15 --aligned_bam $bam
16 --chimeric_junctions $chimeric
17 --left_fq $left_input
18 --right_fq $right_input
19 --denovo_assembler OasesMultiK
20 --out_dir "subdir"
21 </command>
22 <stdio>
23 <exit_code range="1:" level="fatal" description="Error returned from pipeline" />
24 </stdio>
25 <regex match="Must investigate error above."
26 source="stderr"
27 level="fatal"
28 description="Unknown error encountered" />
29 <inputs>
30 <param format="bam" name="bam" type="data" label="Aligned bam" help="Aligned Bam from Star Fusion tool"/>
31 <param format="tabular" name="chimeric" type="data" label="Chimeric.out.junction" help="Chimeric junction from Star Fusion tool"/>
32 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
33 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
34 </inputs>
35 <outputs>
36 <data format="fasta" name="oases.transcripts" label="${tool.name} on ${on_string}: Oasis Transcripts" from_work_dir="subdir/oasesMultiK_out_dir/oases.transcripts.fa" />
37 </outputs>
38 <tests>
39 <test>
40 <!-- The aligned and chimeric I got off of the website don't work with these reads_[1|2].fq.gz inputs.
41 These aligned and chimeric were created when I ran the StarFusion test on these inputs.
42 -->
43 <param name="left_input" value="DISCASM/SF2/reads_1.fq.gz" />
44 <param name="right_input" value="DISCASM/SF2/reads_2.fq.gz" />
45 <param name="bam" value="DISCASM/SF2/Aligned.sortedByCoord.out.bam" />
46 <param name="chimeric" value="DISCASM/SF2/Chimeric.out.junction" />
47 <output name="oases.transcripts" file="DISCASM/reads_1_2.oases.transcripts.fa" />
48 </test>
49 <test>
50 <!-- The Aligned and Chimeric came from a StarFusion test on the reads.[left|right].simPE.fq inputs.
51 -->
52 <param name="left_input" value="DISCASM/SF1/reads.left.simPE.fq" />
53 <param name="right_input" value="DISCASM/SF1/reads.right.simPE.fq" />
54 <param name="bam" value="DISCASM/SF1/SF_out_aligned.bam" />
55 <param name="chimeric" value="DISCASM/SF1/SF_out_chimeric.junction" />
56 <output name="oases.transcripts" file="DISCASM/reads.simPE.oases.transcripts.fa" />
57 </test>
58 </tests>
59 <help>
60 .. class:: infomark
61
62 DISCASM is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR (as run via STAR-Fusion), and supports de novo transcriptome assembly using Trinity or Oases. Please read more here_.
63
64 .. _here: https://github.com/DISCASM/DISCASM/wiki
65 </help>
66 <cite>
67 </cite>
68 </tool>