Mercurial > repos > tyty > structurefold
comparison Iterative_mapping/iterative_map.xml @ 56:9d26c2e4953e draft
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author | tyty |
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date | Tue, 18 Nov 2014 01:00:33 -0500 |
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55:20b8f6ab0e05 | 56:9d26c2e4953e |
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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 $t_end $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 $t_end $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="1.7.1">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="File format 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 nucleotides trimmed each round"/> | |
31 <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/> | |
32 <param name="t_end" type="select" label="Trim from 5' or 3' end"> | |
33 <option value="five_end">5' end</option> | |
34 <option value="three_end">3' end</option> | |
35 </param> | |
36 | |
37 <conditional name="mapping_file"> | |
38 <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)"> | |
39 <option value="default">Default</option> | |
40 <option value="user">User specified</option> | |
41 </param> | |
42 <when value="default"/> | |
43 <when value="user"> | |
44 <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/> | |
45 <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/> | |
46 <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/> | |
47 <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/> | |
48 <param name="param_a" type="boolean" checked="False" truevalue = "1" falsevalue = "0" label="Whether or not to report all valid alignments per read (-a)"/> | |
49 <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"/> | |
50 <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)"/> | |
51 </when> | |
52 </conditional> | |
53 | |
54 </inputs> | |
55 <outputs> | |
56 <data name="output" type="data" format="bam"/> | |
57 </outputs> | |
58 <tests> | |
59 <test> | |
60 <param name="file_format.type" value="fasta" /> | |
61 <param name="file_format.seq_file" value="sample.fasta" /> | |
62 <param name="reference_file" value="rRNA.txt" /> | |
63 <param name="shift" value="1" /> | |
64 <param name="length" value="21" /> | |
65 <param name="mapping_file.type" value="default" /> | |
66 <output name="output" file="mapped.out" /> | |
67 </test> | |
68 </tests> | |
69 | |
70 <help> | |
71 | |
72 | |
73 **TIPS**: | |
74 | |
75 ----- | |
76 | |
77 **Input**: | |
78 | |
79 * 1. Sequence file type (FASTA/FASTQ) | |
80 * 2. Sequence file (fasta/fastq format) | |
81 * 3. Reference file (fasta) used to map the reads to | |
82 * 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping) | |
83 * 5. “Length” (The minimum length of the reads for mapping after trimming) | |
84 * [Optional] | |
85 * 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) | |
86 | |
87 ----- | |
88 | |
89 **Output**: | |
90 | |
91 A bam file with all of the reads that are mapped | |
92 | |
93 | |
94 | |
95 </help> | |
96 </tool> |