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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
author genouest
date Mon, 10 Sep 2018 10:16:42 -0400
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ac738de70427 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
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1 <tool id="get_pairs" name="Separate paired and unpaired reads" version="0.3" >
ac738de70427 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
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2 <!-- author : lecorguille@sb-roscoff.fr -->
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3 <!-- date : 20-11-12 -->
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4 <!-- adapted by abretaud -->
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5
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6 <description>from two fastq files</description>
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8 <requirements>
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9 <requirement type="package" version="3.6">python</requirement>
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10 </requirements>
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ac738de70427 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
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12 <command><![CDATA[
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13 #if $library.type == 'paired':
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14 python '$__tool_directory__/get_pairs.py' '$library.input_left' '$library.input_right'
ac738de70427 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
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15 #else if $library.type == 'paired_collection'
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16 python '$__tool_directory__/get_pairs.py' '$library.input.forward' '$library.input.reverse'
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17 #end if
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18 ]]></command>
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20 <inputs>
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21 <conditional name="library">
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22 <param name="type" type="select" label="Input type">
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23 <option value="paired" selected="true">Independent datasets</option>
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24 <option value="paired_collection">Paired-end collection</option>
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25 </param>
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26
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27 <when value="paired">
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28 <param name="input_left" type="data" format="fastqsanger" label="Forward reads" />
ac738de70427 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
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29 <param name="input_right" type="data" format="fastqsanger" label="Reverse reads" />
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30 </when>
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31
ac738de70427 planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/get_pairs commit 02689a4f03aff06ce7f56ffd329ad72befdc692c
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32 <when value="paired_collection">
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33 <param name="input" format="fastqsanger" type="data_collection" collection_type="paired" label="Paired collection" />
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34 </when>
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35
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36 </conditional>
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37 </inputs>
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38
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39 <outputs>
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40 <data format="fastqsanger" name="left_paired" from_work_dir="left.paired.fastq" label="${tool.name} on ${on_string}: paired forward" />
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41 <data format="fastqsanger" name="right_paired" from_work_dir="right.paired.fastq" label="${tool.name} on ${on_string}: paired reverse" />
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42 <data format="fastqsanger" name="left_unpaired" from_work_dir="left.unpaired.fastq" label="${tool.name} on ${on_string}: unpaired forward" />
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43 <data format="fastqsanger" name="right_unpaired" from_work_dir="right.unpaired.fastq" label="${tool.name} on ${on_string}: unpaired reverse" />
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44 </outputs>
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45 <tests>
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46 <test>
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47 <conditional name="library">
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48 <param name="input_left" value="r1.fastq" />
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49 <param name="input_right" value="r2.fastq" />
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50 </conditional>
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51 <output name="left_paired" file="r1_paired.fastq" />
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52 <output name="right_paired" file="r2_paired.fastq" />
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53 <output name="left_unpaired" file="r1_unpaired.fastq" />
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54 <output name="right_unpaired" file="r2_unpaired.fastq" />
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55 </test>
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56 <test>
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57 <conditional name="library">
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58 <param name="type" value="paired_collection" />
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59 <param name="input">
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60 <collection type="paired">
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61 <element name="forward" ftype="fastq" value="r1.fastq" />
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62 <element name="reverse" ftype="fastq" value="r2.fastq" />
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63 </collection>
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64 </param>
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65 </conditional>
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66 <output name="left_paired" file="r1_paired.fastq" />
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67 <output name="right_paired" file="r2_paired.fastq" />
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68 <output name="left_unpaired" file="r1_unpaired.fastq" />
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69 <output name="right_unpaired" file="r2_unpaired.fastq" />
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70 </test>
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71 </tests>
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72
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73 <help><![CDATA[
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74 A tool to separate paired and unpaired reads from fastq datasets.
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75 ]]></help>
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76 <citations>
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77 </citations>
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78 </tool>