Mercurial > repos > iuc > mothur_heatmap_sim

comparison heatmap.sim.xml @ 3:eb3fcb541aad draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:21:51 -0500
parents 4c752399b0c7
children 861d4d4458e9
comparison
equal deleted inserted replaced
2:42be017bb432 3:eb3fcb541aad
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 "$count" count.dat && 13 ln -s '$count' count.dat &&
14 #if $input.source == 'shared': 14 #if $input.source == 'shared':
15 ln -s "$input.otu" input_otu.dat && 15 ln -s '$input.otu' input_otu.dat &&
16 #else 16 #else
17 ln -s "$input.dist" input_dist.dat && 17 ln -s '$input.dist' input_dist.dat &&
18 #if $input.source == 'column': 18 #if $input.source == 'column':
19 ln -s "$input.name" input_name.dat && 19 ln -s '$input.name' input_name.dat &&
20 #end if 20 #end if
21 #end if
22
23 echo 'heatmap.sim(
24 #if $input.source == "shared":
25 shared=input_otu.dat,
26 #if $input.label:
27 label=${ str($input.label).replace(",","-") },
21 #end if 28 #end if
22 29 #if $input.groups:
23 echo 'heatmap.sim( 30 groups=${ str($input.groups).replace(",","-") },
24 #if $input.source == "shared": 31 #end if
25 shared=input_otu.dat, 32 #if $input.calc:
26 #if $input.label: 33 calc=${ str($input.calc).replace(",","-") },
27 label=${ str($input.label).replace(",","-") }, 34 #end if
28 #end if 35 #elif $input.source == "column":
29 #if $input.groups: 36 column=input_dist.dat,
30 groups=${ str($input.groups).replace(",","-") }, 37 name=input_name.dat,
31 #end if 38 #elif $input.source == "phylip":
32 #if $input.calc: 39 phylip=input_dist.dat,
33 calc=${ str($input.calc).replace(",","-") }, 40 #end if
34 #end if 41 #if $count:
35 #elif $input.source == "column": 42 count=count.dat,
36 column=input_dist.dat, 43 #end if
37 name=input_name.dat, 44 fontsize=$fontsize
38 #elif $input.source == "phylip": 45 )'
39 phylip=input_dist.dat, 46 | sed 's/ //g' ## mothur trips over whitespace
40 #end if 47 | mothur
41 #if $count: 48 | tee mothur.out.log
42 count=count.dat,
43 #end if
44 fontsize=$fontsize
45 )'
46 | sed 's/ //g' ## mothur trips over whitespace
47 | mothur
48 | tee mothur.out.log
49 ]]></command> 49 ]]></command>
50 <inputs> 50 <inputs>
51 <conditional name="input"> 51 <conditional name="input">
52 <param name="source" type="select" label="Generate Heatmap for"> 52 <param name="source" type="select" label="Generate Heatmap for">
53 <option value="shared">shared - Sample Similarity - OTU Shared</option> 53 <option value="shared">shared - Sample Similarity - OTU Shared</option>
113 </test> 113 </test>
114 <test> 114 <test>
115 <param name="source" value="shared"/> 115 <param name="source" value="shared"/>
116 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 116 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
117 <output_collection name="heatmaps" count="72"> 117 <output_collection name="heatmaps" count="72">
118 <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/> 118 <element name="0.55.jest.heatmap">
119 <assert_contents>
120 <has_text text="svg xmlns:svg="/>
121 <has_text text="Heatmap at distance 0.55"/>
122 </assert_contents>
123 </element>
119 </output_collection> 124 </output_collection>
120 <expand macro="logfile-test"/> 125 <expand macro="logfile-test"/>
121 </test> 126 </test>
122 <test> 127 <test>
123 <param name="source" value="shared"/> 128 <param name="source" value="shared"/>
124 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 129 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
125 <param name="label" value="0.03,0.26,0.55"/> 130 <param name="label" value="0.03,0.26,0.55"/>
126 <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/> 131 <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/>
127 <param name="groups" value="forest,pasture"/> 132 <param name="groups" value="forest,pasture"/>
128 <output_collection name="heatmaps" count="30"> 133 <output_collection name="heatmaps" count="30">
129 <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/> 134 <element name="0.03.braycurtis.heatmap">
135 <assert_contents>
136 <has_text text="svg xmlns:svg="/>
137 <has_text text="Heatmap at distance 0.03"/>
138 </assert_contents>
139 </element>
130 </output_collection> 140 </output_collection>
131 <expand macro="logfile-test"/> 141 <expand macro="logfile-test"/>
132 </test> 142 </test>
133 </tests> 143 </tests>
134 <help> 144 <help><![CDATA[
135 <![CDATA[
136 145
137 @MOTHUR_OVERVIEW@ 146 @MOTHUR_OVERVIEW@
138 147
139 **Command Documentation** 148 **Command Documentation**
140 149
145 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix 154 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
146 .. _name: https://www.mothur.org/wiki/Name_file 155 .. _name: https://www.mothur.org/wiki/Name_file
147 .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim 156 .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim
148 157
149 v.1.24.0: Updated to Mothur 1.33, added count parameter 158 v.1.24.0: Updated to Mothur 1.33, added count parameter
150 ]]> 159
151 </help> 160 ]]></help>
152 <expand macro="citations"/> 161 <expand macro="citations"/>
153 </tool> 162 </tool>