Mercurial > repos > iuc > mothur_count_groups

annotate count.groups.xml @ 0:2d98db6098be 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 16:28:23 -0400
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children 13a947a26f7a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2d98db6098be 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_groups" name="Count.groups" version="@WRAPPER_VERSION@.0">
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>counts the number of sequences represented by a specific group or set of groups</description>
2d98db6098be 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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iuc
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4 <import>macros.xml</import>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$group" group.dat &&
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 #if $groupnames.source == "accnos":
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$groupnames.accnos" groupnames.accnos.dat &&
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 #end if
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
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15 echo 'count.groups(
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #if $group.is_of_type("mothur.shared"):
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 shared=group.dat
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #elif $group.is_of_type("mothur.count_table"):
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 count=group.dat
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 #else:
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 group=group.dat
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #end if
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #if $groupnames.source == "groups":
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #if $groupnames.groups:
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 ,groups=$groupnames.groups
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #end if
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #elif $groupnames.source == "accnos":
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 #if $groupnames.accnos:
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 ,accnos=groupnames.accnos.dat
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 #end if
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #end if
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32 )'
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 | sed 's/ //g' ## mothur trips over whitespace
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 | mothur &&
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35
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36 ## parse relevant tool output from logfile to file
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 cat mothur.*.logfile
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 | head -n-7
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 | sed '1,29d'
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 > "$grp_count"
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 ]]></command>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <inputs>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <param name="group" type="data" format="mothur.groups,mothur.shared,mothur.count_table" label="group, shared, or count_table - Group file for sequence count"/>
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44 <conditional name="groupnames">
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45 <param name="source" type="select" label="Filter group names">
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <option value="none">Report on All Groups</option>
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47 <option value="groups">A List of Group Names</option>
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48 <option value="accnos">A History Group Name Accnos Dataset</option>
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49 </param>
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50 <when value="none"/>
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51 <when value="groups">
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 <param name="groups" type="select" label="groups - Pick groups to include" multiple="true">
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53 <help>All groups displayed if none are selected.</help>
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54 <options>
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55 <filter type="data_meta" ref="group" key="groups"/>
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56 </options>
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57 </param>
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58 </when>
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59 <when value="accnos">
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60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
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61 </when>
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62 </conditional>
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63 </inputs>
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64 <outputs>
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65 <expand macro="logfile-output"/>
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66 <data name="grp_count" format="tabular" label="${tool.name} on ${on_string}: group.count"/>
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67 <data name="summary" format="tabular" from_work_dir="group*.summary" label="${tool.name} on ${on_string}: summary"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
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72 <param name="groups" value="forest,pasture"/>
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73 <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
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74 <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
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75 <expand macro="logfile-test"/>
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76 </test>
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77 </tests>
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78 <help>
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79 <![CDATA[
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80
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81 @MOTHUR_OVERVIEW@
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82
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83 **Command Documenation**
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84
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85 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.
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86
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87 .. _shared: http://www.mothur.org/wiki/Shared_file
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88 .. _group: http://www.mothur.org/wiki/Group_file
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89 .. _count.groups: http://www.mothur.org/wiki/Count.groups
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90 ]]>
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91 </help>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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92 <expand macro="citations"/>
2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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93 </tool>