annotate Iterative_mapping/iterative_map.xml @ 3:f4cc06e92530 draft

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author tyty
date Mon, 15 Sep 2014 14:52:20 -0400
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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 $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 $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">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="Format of the file 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 nucleotide 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 <conditional name="mapping_file">
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33 <param name="type" type="select" label="Bowtie mapping flags (Default -v 0 -a --best --strata)">
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34 <option value="default">Default</option>
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35 <option value="user">User specified</option>
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36 </param>
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37 <when value="default"/>
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38 <when value="user">
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39 <param name="param_v" type="integer" value="0" label="Number of mismatches for SOAP-like alignment policy (-v)"/>
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40 <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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41 <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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42 <param name="param_k" type="integer" value="1" label="Report up to n valid alignments per read (-k)"/>
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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)"/>
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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"/>
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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)"/>
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46 </when>
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47 </conditional>
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48
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49 </inputs>
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50 <outputs>
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51 <data name="output" type="data" format="bam"/>
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52 </outputs>
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53
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54 <help>
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55
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56
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57 **TIPS**:
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58
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59 -----
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60
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61 **Input**:
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62
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63 * 1. Sequence file type (FASTA/FASTQ)
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64 * 2. Sequence file (fasta/fastq format) {Default: fastq file}
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65 * 3. Reference file (e.g. cDNA library [fasta])
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66 * 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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67 * 5. “Length” (The minimum length of the reads for mapping after trimming)
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68 * [Optional]
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69 * 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)
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70
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71 -----
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72
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73 **Output**:
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74
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75 A bam file with all of the reads that are mapped
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76
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77
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78
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79 </help>
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80 </tool>