Mercurial > repos > iuc > mothur_count_groups

annotate count.groups.xml @ 3:ed773c45b3d6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:50:47 -0500
parents 13a947a26f7a
children 2b127e170db5
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2d98db6098be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_count_groups" name="Count.groups" version="@WRAPPER_VERSION@.0">
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2 <description>counts the number of sequences represented by a specific group or set of groups</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"/>
1
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$group' group.dat &&
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 #if $groupnames.source == "accnos":
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$groupnames.accnos' groupnames.accnos.dat &&
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 #end if
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17
3
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18 echo 'count.groups(
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 #if $group.is_of_type("mothur.shared"):
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 shared=group.dat
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 #elif $group.is_of_type("mothur.count_table"):
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22 count=group.dat
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23 #else:
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24 group=group.dat
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 #end if
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 #if $groupnames.source == "groups":
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 #if $groupnames.groups:
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28 ,groups=${ str($groupnames.groups).replace(",","-") }
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 #end if
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 #elif $groupnames.source == "accnos":
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 #if $groupnames.accnos:
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 ,accnos=groupnames.accnos.dat
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 #end if
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34 #end if
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35 )'
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36 | sed 's/ //g' ## mothur trips over whitespace
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 | mothur
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38 | tee mothur.out.log &&
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39
3
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40 ## parse relevant tool output from logfile to file
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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41 cat mothur.*.logfile
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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42 | head -n-7
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43 | sed '1,30d'
ed773c45b3d6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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44 > '$grp_count'
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45 ]]></command>
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46 <inputs>
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47 <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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48 <conditional name="groupnames">
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49 <param name="source" type="select" label="Filter group names">
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50 <option value="none">Report on All Groups</option>
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51 <option value="groups">A List of Group Names</option>
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52 <option value="accnos">A History Group Name Accnos Dataset</option>
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53 </param>
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54 <when value="none"/>
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55 <when value="groups">
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56 <param name="groups" type="select" label="groups - Pick groups to include" multiple="true">
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57 <help>All groups displayed if none are selected.</help>
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58 <options>
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59 <filter type="data_meta" ref="group" key="groups"/>
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60 </options>
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61 </param>
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62 </when>
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63 <when value="accnos">
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64 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
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65 </when>
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66 </conditional>
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67 </inputs>
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68 <outputs>
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69 <expand macro="logfile-output"/>
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70 <data name="grp_count" format="tabular" label="${tool.name} on ${on_string}: group.count"/>
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71 <data name="summary" format="tabular" from_work_dir="group*.summary" label="${tool.name} on ${on_string}: summary"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
3
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76 <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
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77 <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
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78 <expand macro="logfile-test"/>
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79 </test>
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80 <test>
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81 <param name="group" value="amazon.an.shared" ftype="mothur.shared"/>
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82 <param name="source" value="groups"/>
0
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83 <param name="groups" value="forest,pasture"/>
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84 <output name="summary" md5="58508af98ed02e00a707f0f7812c2359"/>
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85 <output name="grp_count" md5="34ea2b8be163cf6c9c68d624d92fc73d"/>
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86 <expand macro="logfile-test"/>
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87 </test>
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88 </tests>
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89 <help><![CDATA[
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90
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91 @MOTHUR_OVERVIEW@
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92
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93 **Command Documentation**
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94
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95 The count.groups_ command counts sequences from a specific group or set of groups from a group_ or shared_ file.
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96
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97 .. _shared: https://www.mothur.org/wiki/Shared_file
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98 .. _group: https://www.mothur.org/wiki/Group_file
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99 .. _count.groups: https://www.mothur.org/wiki/Count.groups
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100
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101 ]]></help>
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102 <expand macro="citations"/>
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103 </tool>