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1 <tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1">
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2 <description>post-processing to identify fusion genes</description>
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3 <version_command>tophat-fusion-post --version</version_command>
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4 <requirements>
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5 <requirement type="package">tophat2</requirement>
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6 </requirements>
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7 <command>
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8 ## Set up tophat_out structure.
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9 mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;
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10
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11 ## Set up blast directory structure.
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12 #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
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13 ln -s ${blast_db_path}/ blast;
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14
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15 ## Set up additional files:
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16 ln -s ${blast_db_path}/refGene.txt .;
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17 ln -s ${blast_db_path}/ensGene.txt .;
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18 ln -s ${blast_db_path}/mcl .;
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19
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20 ## Run tophat-fusion-post
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21 tophat-fusion-post -p 22
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22 --num-fusion-reads $num_fusion_reads --num-fusion-pairs $num_fusion_pairs --num-fusion-both $num_fusion_both --fusion-read-mismatches $fusion_read_mismatches --fusion-multireads $fusion_multireads
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23 #if str($is_human) == 'No':
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24 --non-human
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25 #end if
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26
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27 ## Bowtie2 indices.
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28 ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
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29 </command>
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30
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31 <inputs>
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32 <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/>
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33 <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/>
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34 <param name="num_fusion_reads" type="integer" value="3" label="Num Fusion Reads" help="Fusions with at least this many supporting reads will be reported."/>
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35 <param name="num_fusion_pairs" type="integer" value="2" label="Num Fusion Pairs" help="Fusions with at least this many supporting pairs will be reported."/>
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36 <param name="num_fusion_both" type="integer" value="0" label="Num Fusion Reads + Pairs" help="The sum of supporting reads and pairs is at least this number for a fusion to be reported."/>
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37 <param name="fusion_read_mismatches" type="integer" value="2" label="Fusion Read Mismatches" help="Reads support fusions if they map across fusion with at most this many mismatches."/>
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38 <param name="fusion_multireads" type="integer" value="2" label="Reads that map to more than this many places will be ignored." help=""/>
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39 <param name="is_human" type="select" label="Is your data from humans?">
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40 <option value="Yes" selected="True">Yes</option>
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41 <option value="No">No</option>
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42 </param>
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43 </inputs>
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44
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45 <stdio>
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46 <regex match=".*" source="both" level="log" description="tool progress"/>
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47 </stdio>
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48
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49 <outputs>
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50 <data format="txt" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
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51 <data format="html" name="results_html" label="${tool.name} on ${on_string}: html results" from_work_dir="tophatfusion_out/result.html"/>
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52 </outputs>
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53 </tool>
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