Mercurial > repos > iuc > chira_merge

annotate chira_merge.xml @ 13:b5696beaf6d6 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 baafc05b1428cf0ec56a5171c41f2d429a0e0f96"
author iuc
date Thu, 13 Aug 2020 02:43:31 -0400
parents 948f4bc1f030
children 6492560fe1b4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
1 <tool id="chira_merge" name="ChiRA merge" version="@WRAPPER_VERSION@0">
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
2 <description>merge aligned positions</description>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
3 <macros>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
5 </macros>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
6 <expand macro="requirements" />
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
7 <command><![CDATA[
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
8 chira_merge.py
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
9 -b '$alignments'
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
10 #if str($annotation.choice) == "yes":
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
11 -g '$annotation.gtf'
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
12 #end if
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
13 -so '$segment_overlap'
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
14 -lt '$length_threshold'
9
948f4bc1f030 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
iuc
parents: 8
diff changeset
15 -ao '$alignment_overlap'
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
16 #if str($merge.mode) == "blockbuster":
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
17 -bb
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
18 -d '$merge.distance'
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
19 -mc '$merge.min_cluster_height'
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
20 -mb '$merge.min_block_height'
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
21 -sc '$merge.scale'
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
22 #else:
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
23 -ls '$merge.min_locus_size'
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
24 #end if
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
25 #if str($reference.ref_type) == "split":
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
26 -f1 '$reference.ref_fasta1'
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
27 -f2 '$reference.ref_fasta2'
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
28 #end if
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
29 $chimeric_only
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
30 -o ./
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
31 ]]></command>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
32
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
33 <inputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
34 <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
35 <conditional name="annotation">
1
ce26b5a859ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 6845f3b028a42acbefb07c5f59fd2e558f50a768"
iuc
parents: 0
diff changeset
36 <param name="choice" type="select" label="Do you have an annotation in GTF format?">
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
37 <option value="yes">Yes</option>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
38 <option value="no">No</option>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
39 </param>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
40 <when value="yes">
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
41 <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
42 </when>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
43 <when value="no">
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
44 <!-- Do nothing -->
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
45 </when>
0
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
46 </conditional>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
47 <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1"
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
48 help="Matching read positions with greater than this fraction overlap are merged into a segment"/>
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
49 <param name="length_threshold" type="float" value="0.9" label="Minimum length of the alignments as a fraction of longest" min="0" max="1"
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
50 help="Consider the alignments of a that read have at least longer than this value times the longest alignment for that read"/>
9
948f4bc1f030 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
iuc
parents: 8
diff changeset
51 <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments/blocks" min="0" max="1"
948f4bc1f030 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit a69b18084d0a9ade4e29869f8b0e2ce5fc4e0b73"
iuc
parents: 8
diff changeset
52 help="Minimum fraction of BED entries/blockbuster blocks that must overlap inorder to merge"/>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
53 <conditional name="merge">
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
54 <param name="mode" type="select" label="Select the mode of merging">
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
55 <option value="overlap">Overlap based</option>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
56 <option value="blockbuster">Gaussian based (blockbuster)</option>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
57 </param>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
58 <when value="overlap">
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
59 <param name="min_locus_size" type="integer" value="1" label="Minimum locus size"
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
60 help="Minimum number of alignments to be present to output the merged a locus"/>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
61 </when>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
62 <when value="blockbuster">
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
63 <param name="distance" type="integer" value="30" label="Blockbuster parameter distance"
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
64 help="Minimum distance between two clusters"/>
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
65 <param name="min_cluster_height" type="integer" value="10" label="Blockbuster parameter minClusterHeight"
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
66 help="minimum height (readno) of a cluster"/>
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
67 <param name="min_block_height" type="integer" value="10" label="Blockbuster parameter minBlockHeight"
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
68 help="minimum height (readno) of a block"/>
8
c836a05bd6a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit d8a9a5bb648d24f3917951cd7862f449e4dd0688"
iuc
parents: 7
diff changeset
69 <param name="scale" type="float" value="0.1" label="Blockbuster parameter scale" min="0" max="1"
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
70 help="scale stddev for a single read"/>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
71 </when>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
72 </conditional>
7
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
73 <conditional name="reference">
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
74 <param name="ref_type" type="select" label="Did you use single or split reference for alignment?">
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
75 <option value="single">Single reference</option>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
76 <option value="split">Split reference</option>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
77 </param>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
78 <when value="split">
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
79 <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file"
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
80 help="Reference fasta file"/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
81 <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file"
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
82 help="Second reference fasta file."/>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
83 </when>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
84 <when value="single">
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
85 <!-- 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
86 </when>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
87 </conditional>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
88 <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
89 </inputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
90 <outputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
91 <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
92 <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
93 </outputs>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
94
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
95 <tests>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
96 <!-- 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
97 <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
98 <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
99 <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
100 <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
101 <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
102 <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
103 <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
104 <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
105 <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
106 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
107 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
108 <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
109 <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
110 <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
111 <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
112 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
113 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
114 </test>
4
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
115 <!-- 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
116 <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
117 <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
118 <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
119 <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
120 <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
121 <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
122 <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
123 <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
124 <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
125 <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
126 <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
127 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
128 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
129 <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
130 <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
131 <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
132 <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
133 </assert_contents>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
134 </output>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
135 </test>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
136 <!-- 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
137 <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
138 <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
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 <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
146 <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
147 <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
148 <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
149 <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
150 <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
151 </assert_contents>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
152 </output>
0170de5072d4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit aafb8e5de9023eeddd7f4683909f418ef5aae086"
iuc
parents: 1
diff changeset
153 <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
154 <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
155 <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
156 </assert_contents>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
157 </output>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
158 </test>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
159 <!-- 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
160 <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
161 <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
162 <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
163 <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
164 <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
165 <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
166 <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
167 <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
168 <assert_contents>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
169 <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
170 <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
171 </assert_contents>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
172 </output>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
173 <output name="merged_bed" >
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
174 <assert_contents>
35f433d0bd7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
iuc
parents: 4
diff changeset
175 <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"
iuc
parents: 4
diff changeset
176 <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
177 </assert_contents>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
178 </output>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
179 </test>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
180 </tests>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
181
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
182 <help>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
183
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
184 .. class:: infomark
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
185
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
186 **What it does**
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
187
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
188 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.
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
189
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
190 **Inputs**
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
191
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
192 * Alignments in BED format
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
193 * An annotation GTF file contaning reference genomic positions.
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
194
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
195 **Output**
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
196
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
197 * BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned.
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
198 * Tabular file containing merged alignments. 4th column contains all the alignments merged into that location.
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
199
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
200 </help>
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
201 <expand macro="citations" />
5db894671434 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
iuc
parents:
diff changeset
202 </tool>