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comparison Iterative_mapping/iterative_map.xml~ @ 30:4d81d174dece draft

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author tyty
date Mon, 20 Oct 2014 14:44:01 -0400
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29:003096bd038c 30:4d81d174dece
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="0.1.18">samtools</requirement>
13 <requirement type="package" version="0.12.7">bowtie</requirement>
14 </requirements>
15 <inputs>
16 <conditional name="file_format">
17 <param name="type" type="select" label="Format of the file of the reads (Default FASTQ)">
18 <option value="fastq">FASTQ</option>
19 <option value="fasta">FASTA</option>
20 </param>
21 <when value="fastq">
22 <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
23 </when>
24 <when value="fasta">
25 <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
26 </when>
27 </conditional>
28 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
29 <param name="shift" type="integer" value="1" label="Number of nucleotide trimmed each round"/>
30 <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
31 <conditional name="mapping_file">
32 <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
33 <option value="default">Default</option>
34 <option value="user">User specified</option>
35 </param>
36 <when value="default"/>
37 <when value="user">
38 <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
39 <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
40 <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
41 <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
42 <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/>
43 <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"/>
44 <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)"/>
45 </when>
46 </conditional>
47
48 </inputs>
49 <outputs>
50 <data name="output" type="data" format="bam"/>
51 </outputs>
52
53 <help>
54
55
56 **TIPS**:
57
58 -----
59
60 **Input**:
61
62 * 1. Sequence file type (FASTA/FASTQ)
63 * 2. Sequence file (fasta/fastq format) {Default: fastq file}
64 * 3. Reference file (e.g. cDNA library [fasta])
65 * 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
66 * 5. “Length” (The minimum length of the reads for mapping after trimming)
67 * [Optional]
68 * 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)
69
70 -----
71
72 **Output**:
73
74 A bam file with all of the reads that are mapped
75
76
77
78 </help>
79 </tool>