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comparison merge.groups.xml @ 0:ed5f1b592d84 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 16:41:05 -0400
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-1:000000000000 0:ed5f1b592d84
1 <tool profile="16.07" id="mothur_merge_groups" name="Merge.groups" version="@WRAPPER_VERSION@.0">
2 <description>Merge groups in a shared file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11 ln -s "$group" group.dat &&
12 #if $design.source == "hist":
13 ln -s "$design.design_dataset" design_dataset.dat &&
14 #else:
15 ln -s "$generated_design" generated_design.dat &&
16 #end if
17
18 echo 'merge.groups(
19 #if $design.source == "hist":
20 design=design_dataset.dat
21 #else:
22 design=generated_design.dat
23 #end if
24 #if $otu:
25 ,shared=otu.dat
26 #end if
27 #if $group:
28 ,group=group.dat
29 #end if
30 #if $groups:
31 ,groups=${ str($groups).replace(",","-") }
32 #end if
33 #if $label:
34 ,label=${ str($label).replace(",","-") }
35 #end if
36 )'
37 | sed 's/ //g' ## mothur trips over whitespace
38 | mothur
39 ]]></command>
40 <configfiles>
41 <configfile name="generated_design"><![CDATA[
42 #if $design.source == 'build':
43 #for $grouping in $design.groupings:
44 #set grp_str = $grouping.groups.__str__
45 #if grp_str != None and len(grp_str) > 0:
46 #for $grp in grp_str.split(','):
47 $grp $grouping.name
48 #end for
49 #end if
50 #end for
51 #end if
52 ]]></configfile>
53 </configfiles>
54 <inputs>
55 <param name="otu" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared Dataset"/>
56 <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
57 <expand macro="labeloptions"/>
58 </param>
59 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Group Dataset"/>
60 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
61 <options>
62 <filter type="data_meta" ref="otu" key="groups"/>
63 </options>
64 </param>
65 <conditional name="design">
66 <param name="source" type="select" label="Grouping Design from" help="">
67 <option value="hist">Your History</option>
68 <option value="build">Build a grouping design</option>
69 </param>
70 <when value="hist">
71 <param name="design_dataset" type="data" format="tabular" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
72 </when>
73 <when value="build">
74 <repeat name="groupings" title="Grouping">
75 <param name="name" type="text" label="Name for a new combined grouping"/>
76 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping">
77 <options>
78 <filter type="data_meta" ref="otu" key="groups"/>
79 </options>
80 </param>
81 </repeat>
82 </when>
83 </conditional>
84 </inputs>
85 <outputs>
86 <expand macro="logfile-output"/>
87 <data name="merged_shared" format="mothur.shared" from_work_dir="otu*.merge.*" label="${tool.name} on ${on_string}: merge.shared">
88 <filter>otu</filter>
89 </data>
90 <data name="merged_group" format="mothur.groups" from_work_dir="group*.merge.*" label="${tool.name} on ${on_string}: merge.groups">
91 <filter>group</filter>
92 </data>
93 </outputs>
94 <tests>
95 <test><!-- test with shared file -->
96 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
97 <param name="source" value="hist"/>
98 <param name="design_dataset" value="toymothur.design2"/>
99 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
100 <expand macro="logfile-test"/>
101 </test>
102 <test><!-- test with shared file and label and group select -->
103 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
104 <param name="label" value="0.05,0.22,0.38"/>
105 <param name="groups" value="forest,pasture"/>
106 <param name="source" value="hist"/>
107 <param name="design_dataset" value="toymothur.design2"/>
108 <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/>
109 <expand macro="logfile-test"/>
110 </test>
111 <test><!-- test with group file -->
112 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
113 <param name="source" value="hist"/>
114 <param name="design_dataset" value="toymothur.design2"/>
115 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
116 <expand macro="logfile-test"/>
117 </test>
118 <test><!-- test with design creation -->
119 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
120 <param name="source" value="build"/>
121 <repeat name="groupings">
122 <param name="name" value="tardis"/>
123 <param name="groups" value="forest"/>
124 </repeat>
125 <repeat name="groupings">
126 <param name="name" value="dalek"/>
127 <param name="groups" value="pasture"/>
128 </repeat>
129 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
130 <expand macro="logfile-test"/>
131 </test>
132 </tests>
133 <help>
134 <![CDATA[
135
136 @MOTHUR_OVERVIEW@
137
138 **Command Documenation**
139
140 The merge.groups_ command reads a shared_ file and a design file and merges the groups in the shared file that are in the same grouping in the design file.
141
142 A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
143 ======= =======
144 duck bird
145 cow mammal
146 pig mammal
147 goose bird
148 cobra reptile
149 ======= =======
150
151 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
152
153 .. _shared: http://www.mothur.org/wiki/Shared_file
154 .. _merge.groups: http://www.mothur.org/wiki/Merge.groups
155 ]]>
156 </help>
157 <expand macro="citations"/>
158 </tool>