annotate chira_map.xml @ 11:f37ad333627a draft

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