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comparison chira_map.xml @ 6:1d3be7700f70 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
author iuc
date Thu, 07 May 2020 03:39:22 -0400
parents 39bb70c2764e
children 6b83059e8f34
comparison
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5:668f0b2f63ec 6:1d3be7700f70
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 chira_map.py -b 8 chira_map.py -b
9 -a '$alignment.aligner' 9 -a '$alignment.aligner'
10 -i '$query' 10 -i '$query'
11 -b
12 #if str($alignment.aligner) == "bwa": 11 #if str($alignment.aligner) == "bwa":
13 -s '$alignment.stranded' 12 -s '$alignment.stranded'
14 -l1 '$alignment.seed_length1' 13 -l1 '$alignment.seed_length1'
15 -l2 '$alignment.seed_length2' 14 -l2 '$alignment.seed_length2'
16 -s1 '$alignment.align_score1' 15 -s1 '$alignment.align_score1'
17 -s2 '$alignment.align_score2' 16 -s2 '$alignment.align_score2'
17 -ma1 '$alignment.match1'
18 -mm1 '$alignment.mismatch1'
19 -ma2 '$alignment.match2'
20 -mm2 '$alignment.mismatch2'
21 -go1 '$alignment.gapo1'
22 -ge1 '$alignment.gape1'
23 -go2 '$alignment.gapo2'
24 -ge2 '$alignment.gape2'
25 -h1 '$alignment.nhits1'
26 -h2 '$alignment.nhits2'
27
18 #else if str($alignment.aligner) == "clan": 28 #else if str($alignment.aligner) == "clan":
19 -s2 '$alignment.align_score' 29 -s2 '$alignment.align_score'
30 -co '$alignment.chimeric_overlap'
20 #end if 31 #end if
21 #if str($reference.ref_type) == "single": 32 #if str($reference.ref_type) == "single":
22 -f1 '$reference.ref_fasta' 33 -f1 '$reference.ref_fasta'
23 #else if str($reference.ref_type) == "split": 34 #else if str($reference.ref_type) == "split":
24 -f1 '$reference.ref_fasta1' 35 -f1 '$reference.ref_fasta1'
25 -f2 '$reference.ref_fasta2' 36 -f2 '$reference.ref_fasta2'
26 #end if 37 #end if
27 -co '$chimeric_overlap'
28 -p "\${GALAXY_SLOTS:-4}" 38 -p "\${GALAXY_SLOTS:-4}"
29 -o ./ 39 -o ./
30 40
31 ]]></command> 41 ]]></command>
32 42
64 </param> 74 </param>
65 <param name="seed_length1" type="integer" value="12" label="Seed length 1" min="1" 75 <param name="seed_length1" type="integer" value="12" label="Seed length 1" min="1"
66 help="Seed length for 1st mapping iteration. bwa-mem parameter -k"/> 76 help="Seed length for 1st mapping iteration. bwa-mem parameter -k"/>
67 <param name="seed_length2" type="integer" value="6" label="Seed length 2" min="1" 77 <param name="seed_length2" type="integer" value="6" label="Seed length 2" min="1"
68 help="Seed length for 2nd mapping iteration. bwa-mem parameter -k"/> 78 help="Seed length for 2nd mapping iteration. bwa-mem parameter -k"/>
69 <param name="align_score1" type="integer" value="18" label="Minimum alignmnet score 1" min="1" 79 <param name="align_score1" type="integer" value="18" min="1"
70 help="Minimum alignment score in 1st mapping iteration. It 80 label="Minimum alignmnet score for 1st mapping iteration" help="bwa-mem parameter '-T'"/>
71 must be smaller than --align_score1 parameter. bwa-mem parameter '-T'"/> 81 <param name="align_score2" type="integer" value="10" min="1"
72 <param name="align_score2" type="integer" value="10" label="Minimum alignmnet score 2" min="1" 82 label="Minimum alignmnet score for 2nd mapping iteration" help="bwa-mem parameter '-T'"/>
73 help="Minimum alignment score in 2nd mapping iteration. bwa-mem parameter '-T'"/> 83 <param name="match1" type="integer" value="1" label="Matching score for 1st mapping iteration"/>
84 <param name="mismatch1" type="integer" value="4" label="Mismatch penalty for 1st mapping iteration"/>
85 <param name="match2" type="integer" value="1" label="Matching score for 2nd mapping iteration"/>
86 <param name="mismatch2" type="integer" value="7" label="Mismatch penalty for 2nd mapping iteration"/>
87 <param name="gapo1" type="integer" value="6" label="Gap opening penalty for 1st mapping iteration"/>
88 <param name="gape1" type="integer" value="1" label="Gap extension penalty for 1st mapping iteration"/>
89 <param name="gapo2" type="integer" value="100" label="Gap opening penalty for 2nd mapping iteration"/>
90 <param name="gape2" type="integer" value="100" label="Gap extension penalty for 2nd mapping iteration"/>
91 <param name="nhits1" type="integer" value="50"
92 label="Maximum number of allowed multi hits per read in 1st iteration"/>
93 <param name="nhits2" type="integer" value="100"
94 label="Maximum number of allowed multi hits per read in 2nd iteration"/>
74 </when> 95 </when>
75 <when value="clan"> 96 <when value="clan">
76 <param name="align_score" type="integer" value="10" label="Minimum length for each fragment" min="1" 97 <param name="align_score" type="integer" value="10" label="Minimum length for each fragment" min="1"
77 help="Minimu length of the read segment that needs to be mapped. clan_search parameter '-l'"/> 98 help="Minimu length of the read segment that needs to be mapped. clan_search parameter '-l'"/>
99 <param name="chimeric_overlap" type="integer" value="2" label=" Maximum number of bases allowed
100 between the chimericsegments of a read"/>
78 </when> 101 </when>
79 </conditional> 102 </conditional>
80 <param name="chimeric_overlap" type="integer" value="2" label=" Maximum number of bases allowed
81 between the chimericsegments of a read"/>
82 </inputs> 103 </inputs>
83 104
84 <outputs> 105 <outputs>
85 <data format="bed" name="mapped_bed" from_work_dir="mapped.bed" label="ChiRA aligned BED on ${on_string}"/> 106 <data format="bed" name="mapped_bed" from_work_dir="sorted.bed" label="ChiRA aligned BED on ${on_string}"/>
86 <data format="fasta" name="unmapped_fasta" from_work_dir="short.unmapped.fa" 107 <data format="fasta" name="unmapped_fasta" from_work_dir="unmapped.fasta"
87 label="ChiRA unmapped FASTA on ${on_string}"> 108 label="ChiRA unmapped FASTA on ${on_string}">
88 <filter>alignment['aligner'] == "bwa"</filter> 109 <filter>alignment['aligner'] == "bwa"</filter>
89 </data> 110 </data>
90 </outputs> 111 </outputs>
91 112