Mercurial > repos > iuc > mothur_bin_seqs

annotate bin.seqs.xml @ 3:cb91c12c8a34 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ca8dc573528ab7c5290bc6ca029cb989f4755db6
author iuc
date Fri, 08 Sep 2017 12:47:07 -0400
parents c6461f53ded3
children f5cdc7035fd8
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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"/>
1
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
1
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
0
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12 ## create symlinks to input datasets
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13 ln -s "$name" name.dat &&
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14 ln -s "$group" group.dat &&
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15 ln -s "$fasta" fasta.dat &&
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16 ln -s "$otu" otu.dat &&
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17 ln -s "$count" count.dat &&
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18
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19 echo 'bin.seqs(
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20 #if $name:
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21 name=name.dat,
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22 #end if
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23 #if $group:
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24 group=group.dat,
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25 #end if
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26 #if $label:
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27 label=${ str($label).replace(",","-") },
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28 #end if
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29 #if $count:
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30 count=count.dat,
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31 #end if
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32 fasta=fasta.dat,
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33 list=otu.dat
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34 )'
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35 | sed 's/ //g' ## mothur trips over whitespace
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36 | mothur
1
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37 | tee mothur.out.log
0
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38 ]]></command>
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39 <inputs>
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40 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/>
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41 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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42 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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43 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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44 <expand macro="labeloptions"/>
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45 </param>
3
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46 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
0
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47 <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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48 </inputs>
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49 <outputs>
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50 <expand macro="logfile-output"/>
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51 <collection name="fastafiles" type="list" label="${tool.name} on ${on_string}: fastafiles per label">
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52 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
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53 </collection>
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54 </outputs>
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55 <tests>
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56 <test><!-- test with defaults -->
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57 <param name="otu" value="amazon.an.list"/>
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58 <param name="fasta" value="amazon.fasta"/>
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59 <output_collection name="fastafiles" count="36">
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60 <element name="0.22" md5="8fd8dd141561dc3e574e0c3f356e7e84" ftype="fasta"/>
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61 </output_collection>
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62 <expand macro="logfile-test"/>
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63 </test>
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64 <test><!-- test with group and name file and label select -->
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65 <param name="otu" value="amazon.an.list"/>
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66 <param name="fasta" value="amazon.fasta"/>
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67 <param name="name" value="amazon.names"/>
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68 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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69 <param name="label" value="0.03,0.05,0.22"/>
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70 <output_collection name="fastafiles" count="3">
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71 <element name="0.22" md5="02755d06b535fdcdb5a70b6eb767d1f6" ftype="fasta"/>
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72 </output_collection>
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73 <expand macro="logfile-test"/>
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74 </test>
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75 </tests>
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76 <help>
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77 <![CDATA[
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78
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79 @MOTHUR_OVERVIEW@
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80
1
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81 **Command Documentation**
0
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82
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83 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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84
1
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85 .. _list_file: https://www.mothur.org/wiki/List_file
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86 .. _bin.seqs: https://www.mothur.org/wiki/Bin.seqs
0
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87 ]]>
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88 </help>
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89 <expand macro="citations"/>
c9045fb0bf49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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90 </tool>