Mercurial > repos > trinity_ctat > discasm
annotate discasm.xml @ 3:931d2156d896 draft default tip
Adding gmap_fusion tool.
| author | trinity_ctat |
|---|---|
| date | Mon, 22 Jan 2018 16:18:42 -0500 |
| parents | 10a6c3d5a022 |
| children |
| rev | line source |
|---|---|
| 0 | 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> | |
| 1 | 4 <requirement type="package" version="0.1.2">discasm</requirement> |
| 0 | 5 </requirements> |
| 6 <command detect_errors="default"> | |
| 7 DISCASM | |
| 8 --aligned_bam $bam | |
| 9 --chimeric_junctions $chimeric | |
| 10 --left_fq $left_input | |
| 11 --right_fq $right_input | |
| 12 --denovo_assembler OasesMultiK | |
| 13 --out_dir "subdir" | |
| 14 </command> | |
| 15 <stdio> | |
| 16 <exit_code range="1:" level="fatal" description="Error returned from pipeline" /> | |
| 17 </stdio> | |
| 18 <regex match="Must investigate error above." | |
| 19 source="stderr" | |
| 20 level="fatal" | |
| 21 description="Unknown error encountered" /> | |
| 22 <inputs> | |
| 23 <param format="bam" name="bam" type="data" label="Aligned bam" help="Aligned Bam from Star Fusion tool"/> | |
| 24 <param format="tabular" name="chimeric" type="data" label="Chimeric.out.junction" help="Chimeric junction from Star Fusion tool"/> | |
| 25 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/> | |
| 26 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="fasta" name="oases.transcripts" label="${tool.name} on ${on_string}: Oasis Transcripts" from_work_dir="subdir/oasesMultiK_out_dir/oases.transcripts.fa" /> | |
| 30 </outputs> | |
|
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10a6c3d5a022
Updating so that new conda build of discasm will be used.
trinity_ctat
parents:
1
diff
changeset
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31 |
| 0 | 32 <tests> |
| 33 <test> | |
| 34 <!-- The aligned and chimeric I got off of the website don't work with these reads_[1|2].fq.gz inputs. | |
| 35 These aligned and chimeric were created when I ran the StarFusion test on these inputs. | |
| 36 --> | |
| 37 <param name="left_input" value="DISCASM/SF2/reads_1.fq.gz" /> | |
| 38 <param name="right_input" value="DISCASM/SF2/reads_2.fq.gz" /> | |
| 39 <param name="bam" value="DISCASM/SF2/Aligned.sortedByCoord.out.bam" /> | |
| 40 <param name="chimeric" value="DISCASM/SF2/Chimeric.out.junction" /> | |
| 41 <output name="oases.transcripts" file="DISCASM/reads_1_2.oases.transcripts.fa" /> | |
| 42 </test> | |
| 43 <test> | |
| 44 <!-- The Aligned and Chimeric came from a StarFusion test on the reads.[left|right].simPE.fq inputs. | |
| 45 --> | |
| 46 <param name="left_input" value="DISCASM/SF1/reads.left.simPE.fq" /> | |
| 47 <param name="right_input" value="DISCASM/SF1/reads.right.simPE.fq" /> | |
| 48 <param name="bam" value="DISCASM/SF1/SF_out_aligned.bam" /> | |
| 49 <param name="chimeric" value="DISCASM/SF1/SF_out_chimeric.junction" /> | |
| 50 <output name="oases.transcripts" file="DISCASM/reads.simPE.oases.transcripts.fa" /> | |
| 51 </test> | |
| 52 </tests> | |
| 53 <help> | |
| 54 .. class:: infomark | |
| 55 | |
| 56 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_. | |
| 57 | |
| 58 .. _here: https://github.com/DISCASM/DISCASM/wiki | |
| 59 </help> | |
| 60 <cite> | |
| 61 </cite> | |
| 62 </tool> |