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5
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1 <tool id="generate_sliding_windows" name="generate_sliding_windows" version="0.2.0">
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3
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2 <description>Split fasta sequence in nucleotide windows</description>
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0
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3 <requirements>
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4 <requirement type="package" version="1.65">biopython</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9
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10 <command interpreter="python"><![CDATA[
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5
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11 generate_sliding_windows.py --input
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12 #if $refFastaSource.fastaSource == "history":
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13 "$input"
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14 #else
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15 "$refFastaSource.pre_installed_fasta.fields.path"
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16 #end if
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17 --output "$output" --window $window --step $step
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0
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18 ]]></command>
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19 <inputs>
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4
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20 <conditional name="refFastaSource">
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21 <param help="" label="Will you select a fasta sequence from your history or use a pre-installed sequence?" name="fastaSource" type="select">
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22 <option value="history">Use one from the history</option>
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23 <option value="pre_installed">Use a pre-installed fasta sequence</option>
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4
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24 </param>
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5
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25 <when value="pre_installed">
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26 <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="pre_installed_fasta" type="select">
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4
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27 <options from_data_table="all_fasta">
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28 </options>
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29 </param>
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30 </when>
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31 <when value="history">
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32 <param format="fasta" label="Select a fasta file for which you wish to generate a multi-fasta file in a sliding window fashion" name="input" type="data" />
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33 </when>
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34 </conditional>
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0
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35 <param type="integer" name="window" value="21" min="1" label="window size" help="Specifiy the size of the windows that should be generated"/>
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36 <param type="integer" name="step" value="21" min="1" label="step size" help="Specify the distance with which windows should be spaced apart."/>
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37 </inputs>
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38 <outputs>
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3
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39 <data name="output" format="fasta" />
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0
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40 </outputs>
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41 <tests>
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42 <test>
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1
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43 <param name="input" value="EcR_USP_224.fa"/>
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0
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44 <param name="window" value="21"/>
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45 <param name="step" value="21"/>
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3
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46 <output name="output" file="output.fa"/>
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0
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50
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51 Generate fixed size sliding windows in fasta format from multi-fasta sequence.
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52
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3
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53 -----------------------------
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54
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55 Given an input fasta sequence
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56
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57 ::
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58
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59
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60 >input
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61 ATGCATGCATGCATGCATGCATGCATCGATGCATCGATCG
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62
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63 produces the following multi-fasta output with window size 10 and step 5:
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64
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65 ::
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66
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67
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68 >input_start:1_stop:10
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69 ATGCATGCAT
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70 >input_start:6_stop:15
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71 TGCATGCATG
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72 >input_start:11_stop:20
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73 GCATGCATGC
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74 >input_start:16_stop:25
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75 CATGCATGCA
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76 >input_start:21_stop:30
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77 ATGCATCGAT
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78 >input_start:26_stop:35
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79 TCGATGCATC
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80
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81 -------------------------
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82
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0
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83 optional arguments:
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84 -h, --help show this help message and exit
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85 --input INPUT supply an input multi-fasta file.
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86 --output OUTPUT supply an output multi-fasta file. If not specified use
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87 stdout.
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88 --window WINDOW Set the size of the generated windows
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89 --step STEP Set distance between the windows
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90
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91 ]]></help>
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92 </tool>
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