Mercurial > repos > tyty > structurefold
comparison Iterative_mapping/iterative_map.xml~ @ 30:4d81d174dece draft
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author | tyty |
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date | Mon, 20 Oct 2014 14:44:01 -0400 |
parents | fcc92680e802 |
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29:003096bd038c | 30:4d81d174dece |
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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 $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> |