Mercurial > repos > iuc > mothur_get_otulist

annotate get.otulist.xml @ 2:7a922d81eca2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:16:35 -0400
parents 2e6fb8f23d5e
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1 <tool profile="16.07" id="mothur_get_otulist" name="Get.otulist" version="@WRAPPER_VERSION@.0">
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2 <description>Get otus for each distance in a otu list</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="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
7a922d81eca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$otu' otu.dat &&
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14
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15 echo 'get.otulist(
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16 list=otu.dat,
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17 #if $label:
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18 label=${ str($label).replace(",","-") },
7a922d81eca2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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19 #end if
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20 sort=$sort
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21 )'
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22 | sed 's/ //g' ## mothur trips over whitespace
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23 | mothur
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24 | tee mothur.out.log
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25 ]]></command>
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26 <inputs>
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27 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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28 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected.">
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29 <expand macro="labeloptions"/>
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30 </param>
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31 <param name="sort" type="select" label="sort - select the output format"
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32 help="If otu is selected the output will be otu number followed by the list of names in that otu.
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33 If name is selected the output will be a sequence name followed by its otu number">
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34 <option value="otu" selected="true">otu</option>
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35 <option value="name">name</option>
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36 </param>
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37 <expand macro="param-savelog"/>
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38 </inputs>
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39 <outputs>
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40 <expand macro="logfile-output"/>
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41 <collection name="otufiles" type="list" label="${tool.name} on ${on_string}: OTUs per label">
2e6fb8f23d5e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otu" format="mothur.list"/>
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43 </collection>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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48 <output_collection name="otufiles" count="36">
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49 <element name="0.22" md5="9dfa8c449a45d66e7ae6b30b34a821cb" ftype="mothur.list"/>
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50 </output_collection>
2
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51 <param name="savelog" value="true"/>
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52 <expand macro="logfile-test"/>
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53 </test>
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54 <test>
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55 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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56 <param name="label" value="0.03,0.38,0.41,0.45"/>
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57 <output_collection name="otufiles" count="4">
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58 <element name="0.41" md5="b40486b3739a6d5b86459dc17a23c253" ftype="mothur.list"/>
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59 </output_collection>
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60 <param name="savelog" value="true"/>
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61 <expand macro="logfile-test"/>
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62 </test>
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63 </tests>
2
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64 <help><![CDATA[
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65
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66 @MOTHUR_OVERVIEW@
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67
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68
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69 **Command Documentation**
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70
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71 The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU.
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72
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73 .. _get.otulist: https://www.mothur.org/wiki/Get.otulist
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74
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75 v.1.20.0: Updated to Mothur 1.33
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76
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77 ]]></help>
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78 <expand macro="citations"/>
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79 </tool>