annotate chira_map.xml @ 17:7925dd016f53 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
author iuc
date Sun, 19 Dec 2021 15:48:59 +0000
parents 95ddee768b61
children
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17
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1 <tool id="chira_map" name="ChiRA map" version="@TOOL_VERSION@0">
0
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2 <description>map reads to trascriptome</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
17
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6 <expand macro="bio_tools"/>
0
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive"><![CDATA[
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9 chira_map.py -b
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10 -a '$alignment.aligner'
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11 -i '$query'
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12 #if str($alignment.aligner) == "bwa":
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13 -s '$alignment.stranded'
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14 -l1 '$alignment.seed_length1'
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15 -l2 '$alignment.seed_length2'
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16 -s1 '$alignment.align_score1'
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17 -s2 '$alignment.align_score2'
6
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18 -ma1 '$alignment.match1'
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19 -mm1 '$alignment.mismatch1'
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20 -ma2 '$alignment.match2'
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21 -mm2 '$alignment.mismatch2'
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22 -go1 '$alignment.gapo1'
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23 -ge1 '$alignment.gape1'
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24 -go2 '$alignment.gapo2'
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25 -ge2 '$alignment.gape2'
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26 -h1 '$alignment.nhits1'
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27 -h2 '$alignment.nhits2'
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28
0
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29 #else if str($alignment.aligner) == "clan":
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30 -s2 '$alignment.align_score'
6
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31 -co '$alignment.chimeric_overlap'
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32 #end if
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33 #if str($reference.ref_type) == "single":
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34 -f1 '$reference.ref_fasta'
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35 #else if str($reference.ref_type) == "split":
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36 -f1 '$reference.ref_fasta1'
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37 -f2 '$reference.ref_fasta2'
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38 #end if
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39 -p "\${GALAXY_SLOTS:-4}"
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40 -o ./
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41
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42 ]]></command>
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43
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44 <inputs>
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45 <param format="fasta" name="query" type="data" label="Input FASTA file"
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46 help="Input fasta file"/>
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47 <conditional name="reference">
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48 <param name="ref_type" type="select" label="Single or split reference?"
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49 help="Use single if you have all the transcripts in single fasta file. Use split, if you split the
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50 reference into two such that each chimeric read arm corresponds to one of them">
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51 <option value="split">Split reference</option>
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52 <option value="single">Single reference</option>
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53 </param>
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54 <when value="split">
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55 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
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56 help="Reference fasta file"/>
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57 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
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58 help="Second reference fasta file."/>
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59 </when>
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60 <when value="single">
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61 <param format="fasta" name="ref_fasta" type="data" label="Reference FASTA file"
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62 help="Reference fasta file"/>
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63 </when>
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64 </conditional>
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65 <conditional name="alignment" label="Aligner to use">
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66 <param name="aligner" type="select">
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67 <option value="bwa">BWA-MEM</option>
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68 <option value="clan">CLAN</option>
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69 </param>
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70 <when value="bwa">
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71 <param name="stranded" type="select" label="Map reads to">
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72 <option value="fw">Transcript strand only</option>
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73 <option value="rc">Reverse compliment of transcript strand only</option>
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74 <option value="both">Try both strands</option>
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75 </param>
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76 <param name="seed_length1" type="integer" value="12" label="Seed length 1" min="1"
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77 help="Seed length for 1st mapping iteration. bwa-mem parameter -k"/>
8
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78 <param name="seed_length2" type="integer" value="16" label="Seed length 2" min="1"
0
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79 help="Seed length for 2nd mapping iteration. bwa-mem parameter -k"/>
6
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80 <param name="align_score1" type="integer" value="18" min="1"
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81 label="Minimum alignmnet score for 1st mapping iteration" help="bwa-mem parameter '-T'"/>
8
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82 <param name="align_score2" type="integer" value="16" min="1"
6
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83 label="Minimum alignmnet score for 2nd mapping iteration" help="bwa-mem parameter '-T'"/>
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84 <param name="match1" type="integer" value="1" label="Matching score for 1st mapping iteration"/>
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85 <param name="mismatch1" type="integer" value="4" label="Mismatch penalty for 1st mapping iteration"/>
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86 <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"
iuc
parents: 7
diff changeset
87 <param name="mismatch2" type="integer" value="6" label="Mismatch penalty for 2nd mapping iteration"/>
6
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 3
diff changeset
88 <param name="gapo1" type="integer" value="6" label="Gap opening penalty for 1st mapping iteration"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 3
diff changeset
89 <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"
iuc
parents: 3
diff changeset
90 <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"
iuc
parents: 3
diff changeset
91 <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"
iuc
parents: 3
diff changeset
92 <param name="nhits1" type="integer" value="50"
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 3
diff changeset
93 label="Maximum number of allowed multi hits per read in 1st iteration"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 3
diff changeset
94 <param name="nhits2" type="integer" value="100"
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 3
diff changeset
95 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"
iuc
parents:
diff changeset
96 </when>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
97 <when value="clan">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
98 <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"
iuc
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diff changeset
99 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"
iuc
parents: 3
diff changeset
100 <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
parents: 3
diff changeset
101 between the chimericsegments of a read"/>
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
102 </when>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
103 </conditional>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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104 </inputs>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
105
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
106 <outputs>
6
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 3
diff changeset
107 <data format="bed" name="mapped_bed" from_work_dir="sorted.bed" label="ChiRA aligned BED on ${on_string}"/>
1d3be7700f70 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 3
diff changeset
108 <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"
iuc
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109 label="ChiRA unmapped FASTA on ${on_string}">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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110 <filter>alignment['aligner'] == "bwa"</filter>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
111 </data>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
112 </outputs>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
113
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
114 <tests>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
115 <!-- Test: Map with BWA-mem -->
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
116 <test expect_num_outputs="2">
7
6b83059e8f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 6
diff changeset
117 <param name="seed_length1" value="12"/>
6b83059e8f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 6
diff changeset
118 <param name="seed_length2" value="6"/>
6b83059e8f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 6
diff changeset
119 <param name="align_score1" value="18"/>
6b83059e8f34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 6
diff changeset
120 <param name="align_score2" value="10"/>
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
121 <param name="aligner" value="bwa"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
122 <param name="query" value="reads.fasta"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
123 <param name="ref_type" value="split"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
124 <param name="ref_fasta1" value="ref1.fasta"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
125 <param name="ref_fasta2" value="ref2.fasta"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
126 <output name="mapped_bed" >
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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127 <assert_contents>
3
39bb70c2764e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 0
diff changeset
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"
iuc
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129 </assert_contents>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
130 </output>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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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"
iuc
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132 <assert_contents>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
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>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
135 </output>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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136 </test>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
137 <!-- Test: Map with CLAN -->
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
138 <test expect_num_outputs="1">
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
139 <param name="aligner" value="clan"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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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"
iuc
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diff changeset
141 <param name="ref_type" value="split"/>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
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"
iuc
parents: 0
diff changeset
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"
iuc
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144 <output name="mapped_bed" >
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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145 <assert_contents>
3
39bb70c2764e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 0
diff changeset
146 <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"
iuc
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147 </assert_contents>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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148 </output>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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149 </test>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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150 </tests>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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151 <help>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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152
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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153 .. class:: infomark
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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154
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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155 **What it does**
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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156
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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diff changeset
157 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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158
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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159 **Inputs**
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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160
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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161 * 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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162 * 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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163 * 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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diff changeset
164
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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165 **Output**
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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166
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
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167 * BED file containing the alignments
17
7925dd016f53 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
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parents: 16
diff changeset
168 * unmapped FASTA file (only for aligner BWA-MEM)
0
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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169
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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170 </help>
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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171 <expand macro="citations" />
6c398f64ad6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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172 </tool>