Mercurial > repos > iuc > mothur_heatmap_sim

comparison heatmap.sim.xml @ 2:6c7e2e05f606 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 22:14:21 -0400
parents 002aec843953
children
comparison
equal deleted inserted replaced
1:18fc8b11102c 2:6c7e2e05f606
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>
85 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> 85 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
86 </when> 86 </when>
87 </conditional> 87 </conditional>
88 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/> 88 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
89 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/> 89 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/>
90 <expand macro="param-savelog"/>
90 </inputs> 91 </inputs>
91 <outputs> 92 <outputs>
92 <expand macro="logfile-output"/> 93 <expand macro="logfile-output"/>
93 <data name="heatmap" format="svg" from_work_dir="input_dist*.heatmap.sim.svg" label="${tool.name} on ${on_string}: heatmap.sim.svg"> 94 <data name="heatmap" format="svg" from_work_dir="input_dist*.heatmap.sim.svg" label="${tool.name} on ${on_string}: heatmap.sim.svg">
94 <filter>input['source'] != 'shared'</filter> 95 <filter>input['source'] != 'shared'</filter>
107 <has_text text="svg xmlns:svg="/> 108 <has_text text="svg xmlns:svg="/>
108 <has_text text="Heatmap for"/> 109 <has_text text="Heatmap for"/>
109 <has_text text="U68640"/> 110 <has_text text="U68640"/>
110 </assert_contents> 111 </assert_contents>
111 </output> 112 </output>
113 <param name="savelog" value="true"/>
112 <expand macro="logfile-test"/> 114 <expand macro="logfile-test"/>
113 </test> 115 </test>
114 <test> 116 <test>
115 <param name="source" value="shared"/> 117 <param name="source" value="shared"/>
116 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 118 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
117 <output_collection name="heatmaps" count="72"> 119 <output_collection name="heatmaps" count="72">
118 <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/> 120 <element name="0.55.jest.heatmap">
121 <assert_contents>
122 <has_text text="svg xmlns:svg="/>
123 <has_text text="Heatmap at distance 0.55"/>
124 </assert_contents>
125 </element>
119 </output_collection> 126 </output_collection>
127 <param name="savelog" value="true"/>
120 <expand macro="logfile-test"/> 128 <expand macro="logfile-test"/>
121 </test> 129 </test>
122 <test> 130 <test>
123 <param name="source" value="shared"/> 131 <param name="source" value="shared"/>
124 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 132 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
125 <param name="label" value="0.03,0.26,0.55"/> 133 <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"/> 134 <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/>
127 <param name="groups" value="forest,pasture"/> 135 <param name="groups" value="forest,pasture"/>
128 <output_collection name="heatmaps" count="30"> 136 <output_collection name="heatmaps" count="30">
129 <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/> 137 <element name="0.03.braycurtis.heatmap">
138 <assert_contents>
139 <has_text text="svg xmlns:svg="/>
140 <has_text text="Heatmap at distance 0.03"/>
141 </assert_contents>
142 </element>
130 </output_collection> 143 </output_collection>
144 <param name="savelog" value="true"/>
131 <expand macro="logfile-test"/> 145 <expand macro="logfile-test"/>
132 </test> 146 </test>
133 </tests> 147 </tests>
134 <help> 148 <help><![CDATA[
135 <![CDATA[
136 149
137 @MOTHUR_OVERVIEW@ 150 @MOTHUR_OVERVIEW@
138 151
139 **Command Documentation** 152 **Command Documentation**
140 153
145 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix 158 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
146 .. _name: https://www.mothur.org/wiki/Name_file 159 .. _name: https://www.mothur.org/wiki/Name_file
147 .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim 160 .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim
148 161
149 v.1.24.0: Updated to Mothur 1.33, added count parameter 162 v.1.24.0: Updated to Mothur 1.33, added count parameter
150 ]]> 163
151 </help> 164 ]]></help>
152 <expand macro="citations"/> 165 <expand macro="citations"/>
153 </tool> 166 </tool>