Mercurial > repos > iuc > mothur_merge_groups

comparison merge.groups.xml @ 2:0efffd5559c6 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 21:56:48 -0400
parents 4170555c36c1
children 2624af4d11ac
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equal deleted inserted replaced
1:e7aa450e9d86 2:0efffd5559c6
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 ln -s "$group" group.dat && 14 ln -s '$group' group.dat &&
15 #if $design.source == "hist": 15 ln -s '$fasta' fasta.dat &&
16 ln -s "$design.design_dataset" design_dataset.dat && 16 #if $design.source == "hist":
17 #else: 17 ln -s '$design.design_dataset' design_dataset.dat &&
18 ln -s "$generated_design" generated_design.dat && 18 #else:
19 ln -s '$generated_design' generated_design.dat &&
20 #end if
21
22 echo 'merge.groups(
23 #if $design.source == "hist":
24 design=design_dataset.dat
25 #else:
26 design=generated_design.dat
27 #end if
28 #if $otu:
29 ,shared=otu.dat
30 #end if
31 #if $group:
32 #if $group.is_of_type("mothur.groups"):
33 ,group=group.dat
34 #elif $group.is_of_type("mothur.count_table"):
35 ,count=group.dat
19 #end if 36 #end if
20 37 #end if
21 echo 'merge.groups( 38 #if $fasta:
22 #if $design.source == "hist": 39 ,fasta=fasta.dat
23 design=design_dataset.dat 40 #end if
24 #else: 41 #if $groups:
25 design=generated_design.dat 42 ,groups=${ str($groups).replace(",","-") }
26 #end if 43 #end if
27 #if $otu: 44 #if $label:
28 ,shared=otu.dat 45 ,label=${ str($label).replace(",","-") }
29 #end if 46 #end if
30 #if $group: 47 ,method=$method
31 ,group=group.dat 48 )'
32 #end if 49 | sed 's/ //g' ## mothur trips over whitespace
33 #if $groups: 50 | mothur
34 ,groups=${ str($groups).replace(",","-") } 51 | tee mothur.out.log
35 #end if
36 #if $label:
37 ,label=${ str($label).replace(",","-") }
38 #end if
39 )'
40 | sed 's/ //g' ## mothur trips over whitespace
41 | mothur
42 | tee mothur.out.log
43 ]]></command> 52 ]]></command>
44 <configfiles> 53 <configfiles>
45 <configfile name="generated_design"><![CDATA[ 54 <configfile name="generated_design"><![CDATA[
46 #if $design.source == 'build': 55 #if $design.source == 'build':
47 #for $grouping in $design.groupings: 56 #for $grouping in $design.groupings:
58 <inputs> 67 <inputs>
59 <param name="otu" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared Dataset"/> 68 <param name="otu" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared Dataset"/>
60 <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true"> 69 <param name="label" type="select" label="label - Pick OTU Labels to include" optional="true" multiple="true">
61 <expand macro="labeloptions"/> 70 <expand macro="labeloptions"/>
62 </param> 71 </param>
63 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Group Dataset"/> 72 <param name="group" type="data" format="mothur.groups,mothur.count_table" optional="true" label="group or count - Group Dataset or Count Table"/>
73 <param name="fasta" type="data" format="fasta,mothur.align" optional="true" label="Fasta file" help="only valid if you supplied a count file"/>
64 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> 74 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
65 <options> 75 <options>
66 <filter type="data_meta" ref="otu" key="groups"/> 76 <filter type="data_meta" ref="otu" key="groups"/>
67 </options> 77 </options>
78 </param>
79 <param name="method" type="select" label="Merging method">
80 <option value="sum" selected="true"> Sum </option>
81 <option value="average"> Average </option>
82 <option value="median"> Median </option>
68 </param> 83 </param>
69 <conditional name="design"> 84 <conditional name="design">
70 <param name="source" type="select" label="Grouping Design from" help=""> 85 <param name="source" type="select" label="Grouping Design from" help="">
71 <option value="hist">Your History</option> 86 <option value="hist">Your History</option>
72 <option value="build">Build a grouping design</option> 87 <option value="build">Build a grouping design</option>
83 </options> 98 </options>
84 </param> 99 </param>
85 </repeat> 100 </repeat>
86 </when> 101 </when>
87 </conditional> 102 </conditional>
103 <expand macro="param-savelog"/>
88 </inputs> 104 </inputs>
89 <outputs> 105 <outputs>
90 <expand macro="logfile-output"/> 106 <expand macro="logfile-output"/>
91 <data name="merged_shared" format="mothur.shared" from_work_dir="otu*.merge.*" label="${tool.name} on ${on_string}: merge.shared"> 107 <data name="merged_shared" format="mothur.shared" from_work_dir="otu*.merge.*" label="${tool.name} on ${on_string}: merge.shared">
92 <filter>otu</filter> 108 <filter>otu</filter>
99 <test><!-- test with shared file --> 115 <test><!-- test with shared file -->
100 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 116 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
101 <param name="source" value="hist"/> 117 <param name="source" value="hist"/>
102 <param name="design_dataset" value="toymothur.design2"/> 118 <param name="design_dataset" value="toymothur.design2"/>
103 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/> 119 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
120 <param name="savelog" value="true"/>
104 <expand macro="logfile-test"/> 121 <expand macro="logfile-test"/>
105 </test> 122 </test>
106 <test><!-- test with shared file and label and group select --> 123 <test><!-- test with shared file and label and group select -->
107 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 124 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
108 <param name="label" value="0.05,0.22,0.38"/> 125 <param name="label" value="0.05,0.22,0.38"/>
109 <param name="groups" value="forest,pasture"/> 126 <param name="groups" value="forest,pasture"/>
110 <param name="source" value="hist"/> 127 <param name="source" value="hist"/>
111 <param name="design_dataset" value="toymothur.design2"/> 128 <param name="design_dataset" value="toymothur.design2"/>
112 <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/> 129 <output name="merged_shared" md5="11818d535bf88938dc063afca3f95b23" ftype="mothur.shared"/>
130 <param name="savelog" value="true"/>
113 <expand macro="logfile-test"/> 131 <expand macro="logfile-test"/>
114 </test> 132 </test>
115 <test><!-- test with group file --> 133 <test><!-- test with group file -->
116 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 134 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
117 <param name="source" value="hist"/> 135 <param name="source" value="hist"/>
118 <param name="design_dataset" value="toymothur.design2"/> 136 <param name="design_dataset" value="toymothur.design2"/>
119 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/> 137 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
138 <param name="savelog" value="true"/>
139 <expand macro="logfile-test"/>
140 </test>
141 <test><!-- test with count table and fasta file -->
142 <param name="group" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
143 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
144 <param name="method" value="median"/>
145 <param name="source" value="hist"/>
146 <param name="design_dataset" value="toymothur.design2"/>
147 <output name="merged_group" ftype="mothur.groups">
148 <assert_contents>
149 <has_text text="U68589"/>
150 <has_text text="tardis"/>
151 <has_text text="dalek"/>
152 </assert_contents>
153 </output>
154 <param name="savelog" value="true"/>
120 <expand macro="logfile-test"/> 155 <expand macro="logfile-test"/>
121 </test> 156 </test>
122 <test><!-- test with design creation --> 157 <test><!-- test with design creation -->
123 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 158 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
124 <param name="source" value="build"/> 159 <param name="source" value="build"/>
129 <repeat name="groupings"> 164 <repeat name="groupings">
130 <param name="name" value="dalek"/> 165 <param name="name" value="dalek"/>
131 <param name="groups" value="pasture"/> 166 <param name="groups" value="pasture"/>
132 </repeat> 167 </repeat>
133 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/> 168 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
169 <param name="savelog" value="true"/>
134 <expand macro="logfile-test"/> 170 <expand macro="logfile-test"/>
135 </test> 171 </test>
136 </tests> 172 </tests>
137 <help> 173 <help><![CDATA[
138 <![CDATA[
139 174
140 @MOTHUR_OVERVIEW@ 175 @MOTHUR_OVERVIEW@
141 176
142 **Command Documentation** 177 **Command Documentation**
143 178
154 189
155 The Make_Design tool can construct a design file from a Mothur dataset that contains group names. 190 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
156 191
157 .. _shared: https://www.mothur.org/wiki/Shared_file 192 .. _shared: https://www.mothur.org/wiki/Shared_file
158 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups 193 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
159 ]]> 194
160 </help> 195 ]]></help>
161 <expand macro="citations"/> 196 <expand macro="citations"/>
162 </tool> 197 </tool>