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1 <tool id="ctat_gmap_fusion" name="ctat_gmap_fusion" version="1.0.0" profile="17.05">
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2 <description>Fusion-finding Using De novo RNA-Seq Transcript Assemblies</description>
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3 <requirements>
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4 <requirement type="package" version="0.4.0">gmap-fusion</requirement>
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5 </requirements>
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6 <command detect_errors="default">
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7 GMAP-fusion
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8 -T $assembled_trans
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9 --left_fq $left_input
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10 --right_fq $right_input
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11 --genome_lib_dir "${genome_resource_lib.fields.path}"
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12 --output "subdir"
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13 </command>
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14 <stdio>
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15 <exit_code range="1:" level="fatal" description="Error returned from pipeline" />
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16 </stdio>
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17 <regex match="Must investigate error above."
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18 source="stderr"
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19 level="fatal"
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20 description="Unknown error encountered" />
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21 <inputs>
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22 <param format="fasta" name="assembled_trans" type="data" label="Assembled Transcripts (ie. Trinity or DISCASM output)" help="Trinity or DISCASM generated transcript fasta"/>
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23 <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help="Forward strand reads"/>
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24 <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help="Reverse strand reads"/>
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25 <param name="genome_resource_lib" type="select" label="Select a reference genome">
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26 <options from_data_table="ctat_genome_resource_libs">
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27 <filter type="sort_by" column="2" />
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28 <validator type="no_options" message="No indexes are available" />
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29 </options>
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30 </param>
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31 </inputs>
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32 <outputs>
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33 <data format="tabular" name="gmapfusion_candidates" label="${tool.name} on ${on_string}: GMAP-fusion candidates" from_work_dir="subdir/GMAP-fusion.final"/>
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34 </outputs>
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35
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36 <tests>
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37 <test>
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38 <param name="left_input" value="GMAP/reads_1.fq.gz" />
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39 <param name="right_input" value="GMAP/reads_2.fq.gz" />
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40 <param name="assembled_trans" value="GMAP/transcripts.fa" />
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41 <!-- FIX - now that we added the CTAT ref lib path as a parameter, how do we find it for testing?
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42 <param name="genome_resource_lib.fields.path" value="?????" />
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43 -->
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44 <output name="gmapfusion_candidates" file="GMAP/fusion.reads_1_2.final" />
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45 </test>
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46 </tests>
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47
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48 <help>
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49 .. class:: infomark
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50
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51 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_.
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52
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53 .. _here: https://github.com/GMAP-fusion/GMAP-fusion/wiki
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54 </help>
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55 </tool>
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