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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit d2317dff5a89016f18038b97d057f47d949e7808-dirty
author jjohnson
date Sat, 26 Jan 2019 12:53:08 -0500
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1 <?xml version="1.0"?>
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2 <tool id="defuse_trinity_analysis" name="Defuse Trinity" version="@DEFUSE_VERSION@.2">
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3 <description>verify fusions with trinity</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Error" />
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9 </stdio>
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10 <command interpreter="python">defuse_trinity_analysis.py --input $defuse_results --transcripts $trinity_transcripts --peptides $trinity_orfs
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11 --nbases $nbases --min_pep_len $min_pep_len --ticdist $ticdist --readthrough=$readthrough
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12 #if 'matched' in str($outputs).split(','):
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13 --matched="$matched_output"
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14 #end if
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15 #if 'aligned' in str($outputs).split(','):
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16 --transcript_alignment="$aligned_output"
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17 #end if
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18 --output $output
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19 </command>
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20 <inputs>
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21 <param name="defuse_results" type="data" format="defuse.results.tsv" label="Defuse Results file"/>
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22 <param name="trinity_transcripts" type="data" format="fasta" label="TrinityRNAseq: Assembled Transcripts"/>
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23 <param name="trinity_orfs" type="data" format="fasta" label="transcriptsToOrfs: Candidate Peptide Sequences"/>
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24 <param name="nbases" type="integer" value="12" min="1" label="Number of bases on either side of the fusion to compare"/>
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25 <param name="min_pep_len" type="integer" value="100" min="0" label="Minimum length of peptide to report"/>
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26 <param name="ticdist" type="integer" value="1000000" min="0" label="Maximum intrachromosomal distance to be classified a Transcription-induced chimera (TIC)"/>
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27 <param name="readthrough" type="integer" value="4" min="0" label="Number of stop_codons to read through"/>
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28 <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs">
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29 <option value="matched">Matched Fusions Trinity Tanscripts and ORFs Tabular</option>
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30 <option value="aligned">Aligned Fusion and Trinity Transcipts Fasta</option>
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31 </param>
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32 </inputs>
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33 <outputs>
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34 <data name="matched_output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusions Trinity Matched ">
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35 <filter>(outputs and 'matched' in outputs)</filter>
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36 </data>
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37 <data name="aligned_output" metadata_source="defuse_results" format="fasta" label="${tool.name} on ${on_string}: Fusion Trinity Sequences">
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38 <filter>(outputs and 'aligned' in outputs)</filter>
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39 </data>
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40 <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/>
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41 </outputs>
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42 <tests>
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43 </tests>
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44 <help>
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45 **Defuse Results**
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47 Verifies DeFuse_ fusion predictions in results.tsv with TrinityRNAseq_ assembled transcripts and ORFs.
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48
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49 DeFuse provides a total fusion sequence of 200-500 nucleotides (nts) around the fusion breakpoint. This may be insufficient to predict the effect of the fusion on protein production. To get a view of the full transcript containing the fusion, Trinity de novo transcripts from the RNA-seq data are compared with the deFuse fusion sequences using a subsequence around the deFuse indetified fusion breakpoint. The Trinity transcriptToOrfs output provides potential proteins from the projected fusion transcript.
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51 This program relies on the header line of the deFuse results.tsv to determine which columns to use for analysis.
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53 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse
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54 .. _TrinityRNAseq: http://trinityrnaseq.github.io/
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55 </help>
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56 <expand macro="citations">
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57 <citation type="doi">10.1038/nbt.1883</citation>
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58 <citation type="doi">10.1038/s41598-018-36840-z</citation>
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59 </expand>
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60 </tool>