Mercurial > repos > iuc > chira_merge

annotate chira_merge.xml @ 18:9930af9d17f8 draft default tip

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 8064fa653fe73c9432c76783d6c635d86548d538"
author iuc
date Sun, 19 Dec 2021 15:48:19 +0000
parents 6492560fe1b4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
18
9930af9d17f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
iuc
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1 <tool id="chira_merge" name="ChiRA merge" version="@TOOL_VERSION@0">
0
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2 <description>merge aligned positions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
18
9930af9d17f8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
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6 <expand macro="bio_tools"/>
0
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7 <expand macro="requirements" />
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8 <command><![CDATA[
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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9 chira_merge.py
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10 -b '$alignments'
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11 #if str($annotation.choice) == "yes":
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12 -g '$annotation.gtf'
4
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13 #end if
0
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14 -so '$segment_overlap'
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15 -lt '$length_threshold'
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16 -ao '$alignment_overlap'
4
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17 #if str($merge.mode) == "blockbuster":
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18 -bb
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19 -d '$merge.distance'
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20 -mc '$merge.min_cluster_height'
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21 -mb '$merge.min_block_height'
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22 -sc '$merge.scale'
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23 #else:
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24 -ls '$merge.min_locus_size'
4
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25 #end if
7
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26 #if str($reference.ref_type) == "split":
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27 -f1 '$reference.ref_fasta1'
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28 -f2 '$reference.ref_fasta2'
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29 #end if
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30 $chimeric_only
0
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31 -o ./
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32 ]]></command>
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33
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34 <inputs>
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35 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/>
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36 <conditional name="annotation">
1
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37 <param name="choice" type="select" label="Do you have an annotation in GTF format?">
0
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38 <option value="yes">Yes</option>
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39 <option value="no">No</option>
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40 </param>
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41 <when value="yes">
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42 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
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43 </when>
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44 <when value="no">
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45 <!-- Do nothing -->
4
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46 </when>
0
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47 </conditional>
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48 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
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49 help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
8
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50 <param name="length_threshold" type="float" value="0.9" label="Minimum length of the alignments as a fraction of longest" min="0" max="1"
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51 help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/>
9
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52 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments/blocks" min="0" max="1"
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53 help="Minimum fraction of BED entries/blockbuster blocks that must overlap inorder to merge"/>
4
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54 <conditional name="merge">
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55 <param name="mode" type="select" label="Select the mode of merging">
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56 <option value="overlap">Overlap based</option>
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57 <option value="blockbuster">Gaussian based (blockbuster)</option>
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58 </param>
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59 <when value="overlap">
8
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60 <param name="min_locus_size" type="integer" value="1" label="Minimum locus size"
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61 help="Minimum number of alignments to be present to output the merged a locus"/>
4
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62 </when>
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63 <when value="blockbuster">
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64 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"
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65 help="Minimum distance between two clusters"/>
8
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66 <param name="min_cluster_height" type="integer" value="10" label="Blockbuster parameter minClusterHeight"
4
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67 help="minimum height (readno) of a cluster"/>
8
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68 <param name="min_block_height" type="integer" value="10" label="Blockbuster parameter minBlockHeight"
4
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69 help="minimum height (readno) of a block"/>
8
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70 <param name="scale" type="float" value="0.1" label="Blockbuster parameter scale" min="0" max="1"
4
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71 help="scale stddev for a single read"/>
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72 </when>
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73 </conditional>
7
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74 <conditional name="reference">
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75 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
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76 <option value="single">Single reference</option>
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77 <option value="split">Split reference</option>
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78 </param>
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79 <when value="split">
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80 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
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81 help="Reference fasta file"/>
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82 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
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83 help="Second reference fasta file."/>
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84 </when>
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85 <when value="single">
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86 <!-- no need to provide a fasta file -->
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
87 </when>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
88 </conditional>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
89 <param name="chimeric_only" type="boolean" truevalue="-c" falsevalue="" checked="false" />
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
90 </inputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
91 <outputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
92 <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
93 <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
94 </outputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
95
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
96 <tests>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
97 <!-- Test: Merge without annotation -->
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
98 <test expect_num_outputs="2">
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
99 <param name="alignments" value="alignments.bed"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
100 <param name="choice" value="no" />
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
101 <param name="ref_type" value="split"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
102 <param name="ref_fasta1" value="ref1.fasta"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
103 <param name="ref_fasta2" value="ref2.fasta"/>
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
104 <output name="segments_bed" >
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
105 <assert_contents>
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
106 <has_text_matching expression="ENSMUST00000037472\t672\t687\t2\|1\|4,ENSMUST00000037472,672,687,\+,14S15M25S\t1\t\+" />
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
107 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
108 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
109 <output name="merged_bed" >
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
110 <assert_contents>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
111 <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" />
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
112 <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" />
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
113 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
114 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
115 </test>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
116 <!-- Test: Merge with annotation -->
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
117 <test expect_num_outputs="2">
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
118 <param name="alignments" value="alignments.bed" />
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
119 <param name="choice" value="yes" />
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
120 <param name="gtf" value="annotation.gtf" />
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
121 <param name="ref_type" value="split"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
122 <param name="ref_fasta1" value="ref1.fasta"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
123 <param name="ref_fasta2" value="ref2.fasta"/>
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
124 <output name="segments_bed" >
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
125 <assert_contents>
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
126 <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
127 <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" />
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
128 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
129 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
130 <output name="merged_bed" >
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
131 <assert_contents>
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
132 <has_text_matching expression="2\t31033086\t31033109\t-" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
133 <has_text_matching expression="7\t83738820\t83738843\t\+" />
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
134 </assert_contents>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
135 </output>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
136 </test>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
137 <!-- Test: Merge using blockbuster -->
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
138 <test expect_num_outputs="2">
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
139 <param name="alignments" value="alignments.bed" />
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
140 <param name="choice" value="yes" />
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
141 <param name="gtf" value="annotation.gtf" />
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
142 <param name="mode" value="blockbuster" />
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
143 <param name="min_block_height" value="1" />
9
948f4bc1f030 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
iuc
parents: 8
diff changeset
144 <param name="min_cluster_height" value="0" />
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
145 <param name="ref_type" value="split"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
146 <param name="ref_fasta1" value="ref1.fasta"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
147 <param name="ref_fasta2" value="ref2.fasta"/>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
148 <output name="segments_bed" >
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
149 <assert_contents>
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
150 <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
151 <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" />
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
152 </assert_contents>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
153 </output>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
154 <output name="merged_bed" >
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
155 <assert_contents>
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
156 <has_text_matching expression="7\t83738820\t83738843\t\+" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
157 </assert_contents>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
158 </output>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
159 </test>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
160 <!-- Test: Chimeric only without annotation -->
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
161 <test expect_num_outputs="2">
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
162 <param name="alignments" value="alignments.bed"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
163 <param name="choice" value="no" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
164 <param name="ref_type" value="split"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
165 <param name="ref_fasta1" value="ref1.fasta"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
166 <param name="ref_fasta2" value="ref2.fasta"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
167 <param name="chimeric_only" value="true"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
168 <output name="segments_bed" >
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
169 <assert_contents>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
170 <has_text_matching expression="mmu-miR-9-5p\t0\t23\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
171 <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t\+" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
172 </assert_contents>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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173 </output>
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174 <output name="merged_bed" >
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175 <assert_contents>
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176 <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t\+" />
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
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177 <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" />
0
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178 </assert_contents>
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179 </output>
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180 </test>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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181 </tests>
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182
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183 <help>
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184
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185 .. class:: infomark
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186
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187 **What it does**
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188
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189 This tool merges the overlapping aligned positions to define the read concentrated loci. If an annotation GTF file produced, the transcriptomic alignment positions are first converted to their corresponding genomic positions.
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190
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191 **Inputs**
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192
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193 * Alignments in BED format
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194 * An annotation GTF file contaning reference genomic positions.
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195
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196 **Output**
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197
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198 * BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned.
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199 * Tabular file containing merged alignments. 4th column contains all the alignments merged into that location.
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200
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201 </help>
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202 <expand macro="citations" />
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203 </tool>