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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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1 <tool profile="16.07" id="mothur_bin_seqs" name="Bin.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>Order Sequences by OTU</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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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 echo 'bin.seqs(
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10 #if $name:
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11 name=$name,
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12 #end if
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13 #if $group:
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14 group=$group,
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15 #end if
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16 #if $label:
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17 label=${ str($label).replace(",","-") },
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18 #end if
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19 #if $count:
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20 count=$count,
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21 #end if
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22 fasta=$fasta,
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23 list=$otu
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24 )'
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25 | sed 's/ //g' ## mothur trips over whitespace
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26 | mothur &&
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27
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28 ## move output files to correct destination
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29 prefix="$otu" &&
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30 mv mothur.*.logfile "$logfile" &&
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31 mv \${prefix%.dat}*.fasta .
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32 ]]></command>
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33 <inputs>
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34 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
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35 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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36 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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37 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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38 <expand macro="labeloptions"/>
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39 </param>
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40 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/>
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41 <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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42 </inputs>
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43 <outputs>
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44 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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45 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
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46 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
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47 </collection>
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48 </outputs>
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49 <tests>
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50 <test><!-- test with defaults -->
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51 <param name="otu" value="amazon.an.list"/>
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52 <param name="fasta" value="amazon.fasta"/>
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53 <output_collection name="fastafiles" count="36">
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54 <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
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55 </output_collection>
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56 <expand macro="logfile-test"/>
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57 </test>
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58 <test><!-- test with group and name file and label select -->
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59 <param name="otu" value="amazon.an.list"/>
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60 <param name="fasta" value="amazon.fasta"/>
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61 <param name="name" value="amazon.names"/>
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62 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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63 <param name="label" value="0.03,0.05,0.22"/>
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64 <output_collection name="fastafiles" count="3">
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65 <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
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66 </output_collection>
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67 <expand macro="logfile-test"/>
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68 </test>
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69 </tests>
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70 <help>
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71 <![CDATA[
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72
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73 @MOTHUR_OVERVIEW@
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74
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75 **Command Documenation**
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76
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77 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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78
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79 .. _list_file: http://www.mothur.org/wiki/List_file
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80 .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs
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81 ]]>
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82 </help>
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83 <expand macro="citations"/>
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84 </tool>