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comparison upload/Iterative_mapping/iterative_map.xml @ 34:d74ed492efdd draft

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author tyty
date Mon, 20 Oct 2014 14:55:16 -0400
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33:1a92d934f8d1 34:d74ed492efdd
1 <tool id="iterative_map_pipeline" name="Iterative mapping" version="1.0">
2 <description></description>
3 <command interpreter="python">
4 #if $mapping_file.type == "user"
5 iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $mapping_file.type $output $mapping_file.param_v $mapping_file.param_five $mapping_file.param_three $mapping_file.param_k $mapping_file.param_a $mapping_file.param_m $mapping_file.param_best
6 #else
7 iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $mapping_file.type $output
8 #end if
9 </command>
10 <requirements>
11 <requirement type="package" version="1.61">biopython</requirement>
12 <requirement type="package" version="1.7">numpy</requirement>
13 <requirement type="package" version="0.1.18">samtools</requirement>
14 <requirement type="package" version="0.12.7">bowtie</requirement>
15 </requirements>
16 <inputs>
17 <conditional name="file_format">
18 <param name="type" type="select" label="Format of the file of the reads (Default FASTQ)">
19 <option value="fastq">FASTQ</option>
20 <option value="fasta">FASTA</option>
21 </param>
22 <when value="fastq">
23 <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
24 </when>
25 <when value="fasta">
26 <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
27 </when>
28 </conditional>
29 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
30 <param name="shift" type="integer" value="1" label="Number of nucleotide trimmed each round"/>
31 <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
32 <conditional name="mapping_file">
33 <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
34 <option value="default">Default</option>
35 <option value="user">User specified</option>
36 </param>
37 <when value="default"/>
38 <when value="user">
39 <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
40 <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
41 <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
42 <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
43 <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
44 <param name="param_m" type="integer" value="-1" label="Suppress all alignments for a read if more than n reportable alignments exist (-m), -1 for unlimited"/>
45 <param name="param_best" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to make Bowtie guarantee that reported singleton alignments are 'best' in terms of stratum and in terms of the quality values at the mismatched positions (--best --strata)"/>
46 </when>
47 </conditional>
48
49 </inputs>
50 <outputs>
51 <data name="output" type="data" format="bam"/>
52 </outputs>
53 <tests>
54 <test>
55 <param name="file_format.type" value="fasta" />
56 <param name="file_format.seq_file" value="sample.fasta" />
57 <param name="reference_file" value="rRNA.txt" />
58 <param name="shift" value="1" />
59 <param name="length" value="21" />
60 <param name="mapping_file.type" value="default" />
61 <output name="output" file="mapped.out" />
62 </test>
63 </tests>
64
65 <help>
66
67
68 **TIPS**:
69
70 -----
71
72 **Input**:
73
74 * 1. Sequence file type (FASTA/FASTQ)
75 * 2. Sequence file (fasta/fastq format) {Default: fastq file}
76 * 3. Reference file (e.g. cDNA library [fasta])
77 * 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
78 * 5. “Length” (The minimum length of the reads for mapping after trimming)
79 * [Optional]
80 * 1. Bowtie mapping flags (options) [Default: -v 0 -a --best --strata] (-v flag indicates the number of allowed mismatches. use -5/-3 flag to trim nucleotides from 5'/3' end of the reads)
81
82 -----
83
84 **Output**:
85
86 A bam file with all of the reads that are mapped
87
88
89
90 </help>
91 </tool>