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