annotate Iterative_mapping/iterative_map.xml @ 56:9d26c2e4953e draft

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author tyty
date Tue, 18 Nov 2014 01:00:33 -0500
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1 <tool id="iterative_map_pipeline" name="Iterative Mapping" version="1.0">
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2 <description></description>
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3 <command interpreter="python">
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4 #if $mapping_file.type == "user"
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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
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6 #else
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7 iterative_map.py $file_format.type $file_format.seq_file $reference_file $shift $length $t_end $mapping_file.type $output
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8 #end if
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9 </command>
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10 <requirements>
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11 <requirement type="package" version="1.61">biopython</requirement>
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12 <requirement type="package" version="1.7.1">numpy</requirement>
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13 <requirement type="package" version="0.1.18">samtools</requirement>
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14 <requirement type="package" version="0.12.7">bowtie</requirement>
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15 </requirements>
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16 <inputs>
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17 <conditional name="file_format">
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18 <param name="type" type="select" label="File format of the reads (Default FASTQ)">
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19 <option value="fastq">FASTQ</option>
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20 <option value="fasta">FASTA</option>
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21 </param>
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22 <when value="fastq">
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23 <param name="seq_file" type="data" format="fastq" label="Fastq file"/>
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24 </when>
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25 <when value="fasta">
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26 <param name="seq_file" type="data" format="fasta" label="Fasta file"/>
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27 </when>
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28 </conditional>
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29 <param name="reference_file" type="data" format="fasta" label="Reference genome/transcriptome"/>
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30 <param name="shift" type="integer" value="1" label="Number of nucleotides trimmed each round"/>
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31 <param name="length" type="integer" value="21" label="Minimum requirement of read length for mapping"/>
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32 <param name="t_end" type="select" label="Trim from 5' or 3' end">
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33 <option value="five_end">5' end</option>
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34 <option value="three_end">3' end</option>
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35 </param>
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36
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37 <conditional name="mapping_file">
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38 <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
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39 <option value="default">Default</option>
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40 <option value="user">User specified</option>
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41 </param>
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42 <when value="default"/>
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43 <when value="user">
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44 <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
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45 <param name="param_five" type="integer" value="0" label="Trim n bases from high-quality (left) end of each read before alignment (-5)"/>
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46 <param name="param_three" type="integer" value="0" label="Trim n bases from high-quality (right) end of each read before alignment (-3)"/>
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47 <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
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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)"/>
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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"/>
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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)"/>
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51 </when>
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52 </conditional>
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53
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54 </inputs>
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55 <outputs>
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56 <data name="output" type="data" format="bam"/>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="file_format.type" value="fasta" />
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61 <param name="file_format.seq_file" value="sample.fasta" />
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62 <param name="reference_file" value="rRNA.txt" />
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63 <param name="shift" value="1" />
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64 <param name="length" value="21" />
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65 <param name="mapping_file.type" value="default" />
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66 <output name="output" file="mapped.out" />
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67 </test>
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68 </tests>
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69
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70 <help>
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71
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72
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73 **TIPS**:
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74
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75 -----
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76
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77 **Input**:
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78
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79 * 1. Sequence file type (FASTA/FASTQ)
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80 * 2. Sequence file (fasta/fastq format)
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81 * 3. Reference file (fasta) used to map the reads to
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82 * 4. “Shift” (The length of the sequence that will be trimmed at the 3’end of the reads before each round of mapping)
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83 * 5. “Length” (The minimum length of the reads for mapping after trimming)
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84 * [Optional]
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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)
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86
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87 -----
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88
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89 **Output**:
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90
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91 A bam file with all of the reads that are mapped
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92
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93
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94
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95 </help>
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96 </tool>