annotate Iterative_mapping/iterative_map.xml @ 50:6747060cdfe6 draft

Uploaded
author tyty
date Mon, 27 Oct 2014 01:50:00 -0400
parents 6c8f3149dc41
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
49
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
1 <tool id="iterative_map_pipeline" name="Iterative Mapping" version="1.0">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
2 <description></description>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
3 <command interpreter="python">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
4 #if $mapping_file.type == "user"
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
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
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
6 #else
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
7 iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $mapping_file.type $output
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
8 #end if
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
9 </command>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
10 <requirements>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
11 <requirement type="package" version="1.61">biopython</requirement>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
12 <requirement type="package" version="1.7.1">numpy</requirement>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
13 <requirement type="package" version="0.1.18">samtools</requirement>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
14 <requirement type="package" version="0.12.7">bowtie</requirement>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
15 </requirements>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
16 <inputs>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
17 <conditional name="file_format">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
18 <param name="type" type="select" label="File format of the reads (Default FASTQ)">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
19 <option value="fastq">FASTQ</option>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
20 <option value="fasta">FASTA</option>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
21 </param>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
22 <when value="fastq">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
23 <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
24 </when>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
25 <when value="fasta">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
26 <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
27 </when>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
28 </conditional>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
29 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
30 <param name="shift" type="integer" value="1" label="Number of nucleotides trimmed each round"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
31 <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
32 <conditional name="mapping_file">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
33 <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
34 <option value="default">Default</option>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
35 <option value="user">User specified</option>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
36 </param>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
37 <when value="default"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
38 <when value="user">
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
39 <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
40 <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
41 <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
42 <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
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)"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
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"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
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)"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
46 </when>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
47 </conditional>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
48
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
49 </inputs>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
50 <outputs>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
51 <data name="output" type="data" format="bam"/>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
52 </outputs>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
53 <tests>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
54 <test>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
55 <param name="file_format.type" value="fasta" />
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
56 <param name="file_format.seq_file" value="sample.fasta" />
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
57 <param name="reference_file" value="rRNA.txt" />
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
58 <param name="shift" value="1" />
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
59 <param name="length" value="21" />
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
60 <param name="mapping_file.type" value="default" />
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
61 <output name="output" file="mapped.out" />
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
62 </test>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
63 </tests>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
64
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
65 <help>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
66
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
67
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
68 **TIPS**:
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
69
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
70 -----
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
71
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
72 **Input**:
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
73
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
74 * 1. Sequence file type (FASTA/FASTQ)
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
75 * 2. Sequence file (fasta/fastq format)
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
76 * 3. Reference file (fasta) used to map the reads to
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
77 * 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
78 * 5. “Length” (The minimum length of the reads for mapping after trimming)
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
79 * [Optional]
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
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 the nucleotides from 5'/3' end of the reads)
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
81
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
82 -----
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
83
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
84 **Output**:
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
85
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
86 A bam file with all of the reads that are mapped
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
87
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
88
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
89
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
90 </help>
6c8f3149dc41 Uploaded
tyty
parents:
diff changeset
91 </tool>