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comparison mirdeep2/mapper.xml @ 0:5b9519f4b165

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author nikhil-joshi
date Mon, 19 Sep 2011 19:04:41 -0400
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-1:000000000000 0:5b9519f4b165
1 <tool id="mapper" name="Mapping to reference">
2 <description>Mapping using a bowtie index</description>
3
4 <requirements>
5 <requirement type="perl-module">mapper_wrapper.pl</requirement>
6 </requirements>
7
8 <command interpreter="perl">
9 ./mapper_wrapper.pl $bowtie_index_name $output_arf $bowtie_index_name.extra_files_path $reads
10
11 #if $reads.extension.startswith("fastq"):
12 -e
13 #end if
14
15 #if $reads.extension.startswith("fasta"):
16 -c
17 #end if
18
19 #if str($convert_rna) == "convert_rna_true":
20 -i
21 #end if
22
23 #if str($remove_non_atcgun) == "remove_non_atcgun_true":
24 -j
25 #end if
26
27 #if str($adapter_seq) != "":
28 -k $adapter_seq
29 #end if
30
31 #if str($discard_short_reads) != "":
32 -l $discard_short_reads
33 #end if
34
35 #if str($collapse_reads) == "Collapsed Reads Fasta":
36 -m
37 #end if
38
39 #if str($map_mismatch) == "map_mismatch_false":
40 -q
41 #end if
42
43 #if str($map_threshold) != "":
44 -r $map_threshold
45 #end if
46
47 -h -s $output_fasta -n
48 </command>
49
50 <inputs>
51 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Reads" help="Reads in fastq or fasta format"/>
52 <param format="bowtie_html_index" name="bowtie_index_name" type="data" optional="false" label="Bowtie indexed reference" help="Select the bowtie-build run, NOT the fasta reference file you indexed."/>
53
54 <param name="convert_rna" type="boolean" truevalue="convert_rna_true" falsevalue="convert_rna_false" checked="false" label="Convert RNA to DNA alphabet (to map against genome)"/>
55
56 <param name="remove_non_atcgun" type="boolean" truevalue="remove_non_atcgun_true" falsevalue="remove_non_atcgun_false" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N"/>
57
58 <param name="adapter_seq" value="" type="text" optional="true" label="Clip 3' Adapter Sequence (optional)" help="Adapter Sequence can only contain a,c,g,t,u,n,A,C,G,T,U,N">
59 <validator type="regex" message="Adapter can ONLY contain a,c,g,t,u,n,A,C,G,T,U,N">^[ACGTUacgtu]+$</validator>
60 </param>
61
62 <param name="discard_short_reads" value="17" type="integer" optional="false" label="Discard reads shorter than this length (0 for keeping all reads)" help="Note that miRDeep2 requires no reads under 17 in length">
63 <validator type="in_range" min="0" message="Minimum value is 0"/>
64 </param>
65
66 <param name="collapse_reads" type="boolean" truevalue="Collapsed Reads Fasta" falsevalue="Fasta" checked="true" label="Collapse identical reads into one read with count information in sequence header (default)"/>
67
68 <param name="map_mismatch" type="boolean" truevalue="map_mismatch_true" falsevalue="map_mismatch_false" checked="false" label="Map with one mismatch in the seed (mapping takes longer)"/>
69
70 <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome">
71 <validator type="in_range" min="1" message="Minimum value is 1"/>
72 </param>
73 </inputs>
74
75 <outputs>
76 <data format="fasta" name="output_fasta" label="$collapse_reads of ${tool.name} on ${on_string}"/>
77 <data format="arf" name="output_arf" label="Mapping output of ${tool.name} on ${on_string} in ARF format"/>
78 </outputs>
79 </tool>
80