Mercurial > repos > iuc > chira_extract

annotate chira_extract.xml @ 1:de66a3316735 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
author iuc
date Mon, 02 Mar 2020 13:36:23 -0500
parents 0a3107204741
children 061844f6837f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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1 <tool id="chira_extract" name="ChiRA extract" version="@WRAPPER_VERSION@0">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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2 <description>extrat the chimeras</description>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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3 <macros>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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4 <import>macros.xml</import>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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5 </macros>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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6 <expand macro="requirements" />
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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7 <command detect_errors="aggressive"><![CDATA[
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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8 #set $genomic_fasta = ''
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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9 #if str($annotation.annot_choice) == "yes":
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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10 #if str($annotation.fasta_source.fasta_source_selector) == 'history':
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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11 #set $genomic_fasta = '$annotation.fasta_source.fasta'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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12 #else
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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13 #set $genomic_fasta = '$annotation.fasta_source.fasta_id.fields.path'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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14 #end if
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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15 #end if
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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16 chira_extract.py
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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17 -l '$loci'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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18 #if str($annotation.annot_choice) == "yes":
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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19 -g '$annotation.gtf'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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20 #if $hybridize:
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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21 -f '$genomic_fasta'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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22 #end if
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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23 #end if
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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24 -tc '$tpm_cutoff'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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25 -sc '$score_cutoff'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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26 -co '$chimeric_overlap'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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27 #if str($reference.ref_type) == "single":
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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28 -f1 '$ref_fasta'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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29 #else if str($reference.ref_type) == "split":
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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30 -f1 '$ref_fasta1'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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31 -f2 '$ref_fasta2'
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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32 #end if
1
de66a3316735 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
iuc
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33 $hybridize
0
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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34 -p "\${GALAXY_SLOTS:-2}"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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35 -o ./
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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36 ]]></command>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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37
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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38 <inputs>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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39 <param format="tabular" name="loci" type="data" label="File containing CRLs information"/>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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40 <conditional name="annotation">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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41 <param name="annot_choice" type="select" label="Have genomic information?"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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42 help="Selecet Yes if you have an annotation file and provide corresponding genomic fasta file">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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43 <option value="yes">Yes</option>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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44 <option value="no">No</option>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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45 </param>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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46 <when value="yes">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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47 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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48 <conditional name="fasta_source">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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49 <param name="fasta_source_selector" type="select" label="Choose the source for the FASTA file">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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50 <option value="history" selected="true">History</option>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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51 <option value="preloaded">Server indexed files</option>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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52 </param>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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53 <when value="history">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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54 <param name="fasta" type="data" format="fasta" label="FASTA file" />
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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55 </when>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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56 <when value="preloaded">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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57 <param name="fasta_id" type="select">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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58 <options from_data_table="fasta_indexes" />
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59 </param>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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60 </when>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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61 </conditional>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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62 </when>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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63 <when value="no">
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64 <!-- Do nothing -->
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65 </when>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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66 </conditional>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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67 <param name="tpm_cutoff" type="float" value="0" label="TPM cut-off" min="0" max="1"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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68 help="Transcripts with less than this percentile TPMs will be discarded in the final output. [0-1.0]"/>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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69 <param name="score_cutoff" type="float" value="0" label="Score cut-off" min="0" max="2"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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70 help="Hybrids with less than this score will be discarded in the final output. [0-2.0]"/>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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71 <param name="chimeric_overlap" type="integer" value="2"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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72 label=" Maximum number of bases allowed between the chimericsegments of a read"/>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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73 <conditional name="reference">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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74 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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75 <option value="split">Split reference</option>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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76 <option value="single">Single reference</option>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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77 </param>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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78 <when value="split">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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79 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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80 help="Reference fasta file"/>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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81 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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82 help="Second reference fasta file."/>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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83 </when>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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84 <when value="single">
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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85 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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86 help="Reference fasta file"/>
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87 </when>
0a3107204741 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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88 </conditional>
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89 <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false" />
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90 </inputs>
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91
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92 <outputs>
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93 <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
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94 <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
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95 </outputs>
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96
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97 <tests>
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98 <test expect_num_outputs="2">
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99 <param name="loci" value="loci.counts"/>
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100 <param name="ref_type" value="split"/>
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101 <param name="ref_fasta1" value="ref1.fasta"/>
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102 <param name="ref_fasta2" value="ref2.fasta"/>
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103 <param name="annot_choice" value="no"/>
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104 <param name="hybridize" value="true" />
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105 <output name="chimeras" file="chimeras" sort="True"/>
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106 <output name="singletons" file="singletons" sort="True"/>
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107 </test>
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108 </tests>
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109 <help>
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110
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111 .. class:: infomark
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112
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113 **What it does**
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114
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115 This tool extracts the best chimeric alignments for each read. User can optionally hybridize the loci where the chimeric arms are mapping to.
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116
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117 **Inputs**
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118
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119 * Tabular file containing CRLs information
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120 * Annotation GTF file
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121 * Reference fasta files. Provide both in case of split reference.
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122 * If your alignments are merged at genomic level in previous step (chira merge), then provide a reference genomic fasta fille.
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123
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124 **Output**
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125
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126 * Tabular file containing chimeras information
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127 </help>
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128 <expand macro="citations" />
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129 </tool>
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130