Mercurial > repos > iuc > chira_map

annotate chira_map.xml @ 11:f37ad333627a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
author iuc
date Thu, 02 Jul 2020 08:53:43 -0400
parents b91f9fcd9fc7
children 95ddee768b61
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6c398f64ad6a "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_map" name="ChiRA map" version="@WRAPPER_VERSION@0">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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2 <description>map reads to trascriptome</description>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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3 <macros>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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4 <import>macros.xml</import>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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5 </macros>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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6 <expand macro="requirements" />
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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7 <command detect_errors="aggressive"><![CDATA[
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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8 chira_map.py -b
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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9 -a '$alignment.aligner'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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10 -i '$query'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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11 #if str($alignment.aligner) == "bwa":
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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12 -s '$alignment.stranded'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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13 -l1 '$alignment.seed_length1'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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14 -l2 '$alignment.seed_length2'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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15 -s1 '$alignment.align_score1'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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16 -s2 '$alignment.align_score2'
6
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17 -ma1 '$alignment.match1'
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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18 -mm1 '$alignment.mismatch1'
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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19 -ma2 '$alignment.match2'
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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20 -mm2 '$alignment.mismatch2'
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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21 -go1 '$alignment.gapo1'
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22 -ge1 '$alignment.gape1'
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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23 -go2 '$alignment.gapo2'
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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24 -ge2 '$alignment.gape2'
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25 -h1 '$alignment.nhits1'
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26 -h2 '$alignment.nhits2'
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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27
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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28 #else if str($alignment.aligner) == "clan":
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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29 -s2 '$alignment.align_score'
6
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30 -co '$alignment.chimeric_overlap'
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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31 #end if
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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32 #if str($reference.ref_type) == "single":
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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33 -f1 '$reference.ref_fasta'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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34 #else if str($reference.ref_type) == "split":
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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35 -f1 '$reference.ref_fasta1'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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36 -f2 '$reference.ref_fasta2'
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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37 #end if
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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38 -p "\${GALAXY_SLOTS:-4}"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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39 -o ./
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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40
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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41 ]]></command>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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42
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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43 <inputs>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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44 <param format="fasta" name="query" type="data" label="Input FASTA file"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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45 help="Input fasta file"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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46 <conditional name="reference">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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47 <param name="ref_type" type="select" label="Single or split reference?"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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48 help="Use single if you have all the transcripts in single fasta file. Use split, if you split the
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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49 reference into two such that each chimeric read arm corresponds to one of them">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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50 <option value="split">Split reference</option>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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51 <option value="single">Single reference</option>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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52 </param>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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53 <when value="split">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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54 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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55 help="Reference fasta file"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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56 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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57 help="Second reference fasta file."/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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58 </when>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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59 <when value="single">
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60 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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61 help="Reference fasta file"/>
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62 </when>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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63 </conditional>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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64 <conditional name="alignment" label="Aligner to use">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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65 <param name="aligner" type="select">
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66 <option value="bwa">BWA-MEM</option>
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67 <option value="clan">CLAN</option>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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68 </param>
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69 <when value="bwa">
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70 <param name="stranded" type="select" label="Map reads to">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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71 <option value="fw">Transcript strand only</option>
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72 <option value="rc">Reverse compliment of transcript strand only</option>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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73 <option value="both">Try both strands</option>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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74 </param>
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75 <param name="seed_length1" type="integer" value="12" label="Seed length 1" min="1"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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76 help="Seed length for 1st mapping iteration. bwa-mem parameter -k"/>
8
b91f9fcd9fc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
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77 <param name="seed_length2" type="integer" value="16" label="Seed length 2" min="1"
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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78 help="Seed length for 2nd mapping iteration. bwa-mem parameter -k"/>
6
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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79 <param name="align_score1" type="integer" value="18" min="1"
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80 label="Minimum alignmnet score for 1st mapping iteration" help="bwa-mem parameter '-T'"/>
8
b91f9fcd9fc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
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81 <param name="align_score2" type="integer" value="16" min="1"
6
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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82 label="Minimum alignmnet score for 2nd mapping iteration" help="bwa-mem parameter '-T'"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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83 <param name="match1" type="integer" value="1" label="Matching score for 1st mapping iteration"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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84 <param name="mismatch1" type="integer" value="4" label="Mismatch penalty for 1st mapping iteration"/>
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85 <param name="match2" type="integer" value="1" label="Matching score for 2nd mapping iteration"/>
8
b91f9fcd9fc7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
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86 <param name="mismatch2" type="integer" value="6" label="Mismatch penalty for 2nd mapping iteration"/>
6
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87 <param name="gapo1" type="integer" value="6" label="Gap opening penalty for 1st mapping iteration"/>
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88 <param name="gape1" type="integer" value="1" label="Gap extension penalty for 1st mapping iteration"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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89 <param name="gapo2" type="integer" value="100" label="Gap opening penalty for 2nd mapping iteration"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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90 <param name="gape2" type="integer" value="100" label="Gap extension penalty for 2nd mapping iteration"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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91 <param name="nhits1" type="integer" value="50"
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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92 label="Maximum number of allowed multi hits per read in 1st iteration"/>
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93 <param name="nhits2" type="integer" value="100"
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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parents: 3
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94 label="Maximum number of allowed multi hits per read in 2nd iteration"/>
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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diff changeset
95 </when>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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96 <when value="clan">
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97 <param name="align_score" type="integer" value="10" label="Minimum length for each fragment" min="1"
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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98 help="Minimu length of the read segment that needs to be mapped. clan_search parameter '-l'"/>
6
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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99 <param name="chimeric_overlap" type="integer" value="2" label=" Maximum number of bases allowed
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
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diff changeset
100 between the chimericsegments of a read"/>
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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101 </when>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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102 </conditional>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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103 </inputs>
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104
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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105 <outputs>
6
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106 <data format="bed" name="mapped_bed" from_work_dir="sorted.bed" label="ChiRA aligned BED on ${on_string}"/>
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107 <data format="fasta" name="unmapped_fasta" from_work_dir="unmapped.fasta"
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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108 label="ChiRA unmapped FASTA on ${on_string}">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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109 <filter>alignment['aligner'] == "bwa"</filter>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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110 </data>
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111 </outputs>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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112
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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113 <tests>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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114 <!-- Test: Map with BWA-mem -->
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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115 <test expect_num_outputs="2">
7
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116 <param name="seed_length1" value="12"/>
6b83059e8f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
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117 <param name="seed_length2" value="6"/>
6b83059e8f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
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118 <param name="align_score1" value="18"/>
6b83059e8f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
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parents: 6
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119 <param name="align_score2" value="10"/>
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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120 <param name="aligner" value="bwa"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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121 <param name="query" value="reads.fasta"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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122 <param name="ref_type" value="split"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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123 <param name="ref_fasta1" value="ref1.fasta"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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124 <param name="ref_fasta2" value="ref2.fasta"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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125 <param name="unmapped" value="True"/>
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126 <output name="mapped_bed" >
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127 <assert_contents>
3
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128 <has_text_matching expression="mmu-miR-6898-5p\t11\t21\t2\|2,mmu-miR-6898-5p,11,21,\+,10M39S\t1\t\+" />
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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129 </assert_contents>
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130 </output>
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131 <output name="unmapped_fasta" >
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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132 <assert_contents>
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133 <has_text_matching expression="AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC" />
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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134 </assert_contents>
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135 </output>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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136 </test>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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137 <!-- Test: Map with CLAN -->
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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138 <test expect_num_outputs="1">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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139 <param name="aligner" value="clan"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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140 <param name="query" value="reads.fasta"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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141 <param name="ref_type" value="split"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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142 <param name="ref_fasta1" value="ref1.fasta"/>
3
39bb70c2764e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
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parents: 0
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143 <param name="ref_fasta2" value="ref2.fasta"/>
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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144 <param name="unmapped" value="True"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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145 <output name="mapped_bed" >
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146 <assert_contents>
3
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147 <has_text_matching expression="mmu-miR-20a-5p\t0\t23\t3\|2,mmu-miR-20a-5p,0,23,\+,5S23M27S\t1\t\+" />
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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148 </assert_contents>
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149 </output>
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150 </test>
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151 </tests>
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152 <help>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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153
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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154 .. class:: infomark
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155
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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156 **What it does**
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157
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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158 This tool handles the mapping of the reads to reference transcriptome. User can choose between the bwa-mem and CLAN alignment tools.
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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159
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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160 **Inputs**
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161
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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162 * A fasta file containing reads
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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163 * A reference fasta file containing transcript sequences
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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164 * An optional second reference fasta file, incase if you split your reference into two
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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165
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166 **Output**
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167
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168 * BED file containing the alignments
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169 * Optional unmapped FASTA file
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170
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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171 </help>
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172 <expand macro="citations" />
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173 </tool>