Mercurial > repos > iuc > mothur_merge_groups

comparison merge.groups.xml @ 3:8ae8f906cfe9 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 09:31:45 -0500
parents 8e771931d548
children a681637e47bb
comparison
equal deleted inserted replaced
2:f0ce762bafb0 3:8ae8f906cfe9
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>
117 <param name="source" value="hist"/> 132 <param name="source" value="hist"/>
118 <param name="design_dataset" value="toymothur.design2"/> 133 <param name="design_dataset" value="toymothur.design2"/>
119 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/> 134 <output name="merged_group" md5="023ebd0668522e9531da5b061e6e9137" ftype="mothur.groups"/>
120 <expand macro="logfile-test"/> 135 <expand macro="logfile-test"/>
121 </test> 136 </test>
137 <test><!-- test with count table and fasta file -->
138 <param name="group" value="amazon_withgroups.count_table" ftype="mothur.count_table"/>
139 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
140 <param name="method" value="median"/>
141 <param name="source" value="hist"/>
142 <param name="design_dataset" value="toymothur.design2"/>
143 <output name="merged_group" ftype="mothur.groups">
144 <assert_contents>
145 <has_text text="U68589"/>
146 <has_text text="tardis"/>
147 <has_text text="dalek"/>
148 </assert_contents>
149 </output>
150 <expand macro="logfile-test"/>
151 </test>
122 <test><!-- test with design creation --> 152 <test><!-- test with design creation -->
123 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 153 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
124 <param name="source" value="build"/> 154 <param name="source" value="build"/>
125 <repeat name="groupings"> 155 <repeat name="groupings">
126 <param name="name" value="tardis"/> 156 <param name="name" value="tardis"/>
132 </repeat> 162 </repeat>
133 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/> 163 <output name="merged_shared" md5="60f9e715c948911a61986bf1d1db7747" ftype="mothur.shared"/>
134 <expand macro="logfile-test"/> 164 <expand macro="logfile-test"/>
135 </test> 165 </test>
136 </tests> 166 </tests>
137 <help> 167 <help><![CDATA[
138 <![CDATA[
139 168
140 @MOTHUR_OVERVIEW@ 169 @MOTHUR_OVERVIEW@
141 170
142 **Command Documentation** 171 **Command Documentation**
143 172
154 183
155 The Make_Design tool can construct a design file from a Mothur dataset that contains group names. 184 The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
156 185
157 .. _shared: https://www.mothur.org/wiki/Shared_file 186 .. _shared: https://www.mothur.org/wiki/Shared_file
158 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups 187 .. _merge.groups: https://www.mothur.org/wiki/Merge.groups
159 ]]> 188
160 </help> 189 ]]></help>
161 <expand macro="citations"/> 190 <expand macro="citations"/>
162 </tool> 191 </tool>