Mercurial > repos > iuc > mothur_bin_seqs

annotate bin.seqs.xml @ 0:c9045fb0bf49 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 17:31:47 -0400
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children c6461f53ded3
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c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Order Sequences by OTU</description>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$name" name.dat &&
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$group" group.dat &&
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$fasta" fasta.dat &&
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$otu" otu.dat &&
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$count" count.dat &&
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15
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16 echo 'bin.seqs(
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #if $name:
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18 name=name.dat,
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19 #end if
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20 #if $group:
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21 group=group.dat,
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #end if
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23 #if $label:
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24 label=${ str($label).replace(",","-") },
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #end if
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #if $count:
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 count=count.dat,
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #end if
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 fasta=fasta.dat,
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 list=otu.dat
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31 )'
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32 | sed 's/ //g' ## mothur trips over whitespace
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33 | mothur
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34 ]]></command>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <inputs>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <param name="label" type="select" label="label - OTU Labels" multiple="true">
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <expand macro="labeloptions"/>
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41 </param>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Represents the number of duplicate sequences for a given representitive sequence"/>
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44 </inputs>
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45 <outputs>
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46 <expand macro="logfile-output"/>
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47 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
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48 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
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49 </collection>
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50 </outputs>
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51 <tests>
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52 <test><!-- test with defaults -->
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53 <param name="otu" value="amazon.an.list"/>
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54 <param name="fasta" value="amazon.fasta"/>
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55 <output_collection name="fastafiles" count="36">
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56 <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
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57 </output_collection>
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58 <expand macro="logfile-test"/>
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59 </test>
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60 <test><!-- test with group and name file and label select -->
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61 <param name="otu" value="amazon.an.list"/>
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62 <param name="fasta" value="amazon.fasta"/>
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63 <param name="name" value="amazon.names"/>
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64 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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65 <param name="label" value="0.03,0.05,0.22"/>
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66 <output_collection name="fastafiles" count="3">
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67 <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
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68 </output_collection>
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69 <expand macro="logfile-test"/>
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74
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75 @MOTHUR_OVERVIEW@
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76
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77 **Command Documenation**
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78
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79 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences.
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80
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81 .. _list_file: http://www.mothur.org/wiki/List_file
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82 .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs
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83 ]]>
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84 </help>
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85 <expand macro="citations"/>
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86 </tool>