Mercurial > repos > iuc > mothur_count_seqs

annotate count.seqs.xml @ 0:be91d6962b0c 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 16:28:37 -0400
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children cb4e005b8e8d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_count_seqs" name="Count.seqs" version="@WRAPPER_VERSION@.0">
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>(aka make.table) counts the number of sequences represented by the representative</description>
be91d6962b0c 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>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
be91d6962b0c 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
be91d6962b0c 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 &&
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 #if $grouping.use == "yes":
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12 ln -s "$grouping.group" grouping.group.dat &&
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 #end if
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 echo 'count.seqs(
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 name=name.dat,
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17 #if $grouping.use == "yes":
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 group=grouping.group.dat,
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #if $grouping.groups:
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20 groups=$grouping.groups,
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #end if
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22 #end if
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23 large=$large
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 )'
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 | sed 's/ //g' ## mothur trips over whitespace
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 | mothur
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 ]]></command>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <inputs>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <conditional name="grouping">
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <param name="use" type="select" label="Use a Group file to include counts for groups">
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <option value="no" selected="true">no</option>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <option value="yes">yes</option>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 </param>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <when value="yes">
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <param name="groups" type="select" label="groups - Groups to display" multiple="true">
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <help>All groups displayed if none are selected.</help>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <options>
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40 <filter type="data_meta" ref="group" key="groups"/>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 </options>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 </param>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 </when>
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44 <when value="no"/>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 </conditional>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
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47 </inputs>
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48 <outputs>
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49 <expand macro="logfile-output"/>
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50 <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 </outputs>
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52 <tests>
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53 <test><!-- test default params -->
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54 <param name="name" value="amazon.names"/>
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55 <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/>
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56 <expand macro="logfile-test"/>
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57 </test>
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58 <test><!-- test with group file -->
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59 <param name="name" value="amazon.names"/>
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60 <param name="use" value="yes"/>
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61 <param name="group" value="amazon.groups"/>
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62 <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/>
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63 <expand macro="logfile-test"/>
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64 </test>
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65 <test> <!-- test with group file and subset of groups -->
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66 <param name="name" value="amazon.names"/>
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67 <param name="use" value="yes"/>
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68 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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69 <param name="groups" value="pasture"/>
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70 <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
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71 <expand macro="logfile-test"/>
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72 </test>
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73 </tests>
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74 <help>
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75 <![CDATA[
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76
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77 @MOTHUR_OVERVIEW@
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78
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79 **Command Documenation**
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80
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81 The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown.
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82
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83 .. _name: http://www.mothur.org/wiki/Name_file
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84 .. _group: http://www.mothur.org/wiki/Group_file
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85 .. _count.seqs: http://www.mothur.org/wiki/Count.seqs
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86 .. _count_table: http://www.mothur.org/wiki/Count_File
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87
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88 v.1.21.0: Updated to Mothur 1.33
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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89 ]]>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 </help>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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91 <expand macro="citations"/>
be91d6962b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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92 </tool>