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comparison dist.shared.xml @ 3:3257183be791 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 09:49:21 -0500
parents 566e0fba8f4b
children 7c8b0d0d792a
comparison
equal deleted inserted replaced
2:beed3d29e380 3:3257183be791
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 14
15 echo 'dist.shared( 15 echo 'dist.shared(
16 shared=otu.dat, 16 shared=otu.dat,
17 #if $label: 17 #if $label:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 #if $groups: 20 #if $groups:
21 groups=${ str($groups).replace(",","-") }, 21 groups=${ str($groups).replace(",","-") },
22 #end if 22 #end if
23 #if $calc: 23 #if $calc:
24 calc=${ str($calc).replace(",","-") }, 24 calc=${ str($calc).replace(",","-") },
25 #end if 25 #end if
26 #if $subsampling.use == "yes": 26 #if $subsampling.use == "yes":
27 #if $subsampling.subsample: 27 #if $subsampling.subsample:
28 subsample=$subsampling.subsample, 28 subsample=$subsampling.subsample,
29 #end if 29 #else
30 iters=$subsampling.iters, 30 subsample=T,
31 #end if 31 #end if
32 output=$output, 32 iters=$subsampling.iters,
33 processors='\${GALAXY_SLOTS:-8}' 33 #end if
34 )' 34 output=$output,
35 | sed 's/ //g' ## mothur trips over whitespace 35 processors='\${GALAXY_SLOTS:-8}'
36 | mothur 36 )'
37 | tee mothur.out.log 37 | sed 's/ //g' ## mothur trips over whitespace
38 | mothur
39 | tee mothur.out.log
38 ]]></command> 40 ]]></command>
39 <inputs> 41 <inputs>
40 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 42 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
41 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true"> 43 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true">
42 <expand macro="labeloptions"/> 44 <expand macro="labeloptions"/>
56 <param name="use" type="select" label="subsample"> 58 <param name="use" type="select" label="subsample">
57 <option value="no" selected="true">no</option> 59 <option value="no" selected="true">no</option>
58 <option value="yes">yes</option> 60 <option value="yes">yes</option>
59 </param> 61 </param>
60 <when value="yes"> 62 <when value="yes">
61 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/> 63 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)"
64 help="Should not exceed the number of sequences in any group"/>
62 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> 65 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
63 </when> 66 </when>
64 <when value="no"/> 67 <when value="no"/>
65 </conditional> 68 </conditional>
66 <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair"> 69 <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
90 <output_collection name="distfiles" count="74"> 93 <output_collection name="distfiles" count="74">
91 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/> 94 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
92 </output_collection> 95 </output_collection>
93 <expand macro="logfile-test"/> 96 <expand macro="logfile-test"/>
94 </test> 97 </test>
95 <test><!-- test with subsampling --> 98 <test><!-- test with subsampling without specifying size -->
96 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 99 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
100 <param name="label" value="0.03,0.33"/>
97 <param name="use" value="yes"/> 101 <param name="use" value="yes"/>
98 <param name="subsample" value="10"/>
99 <param name="iters" value="42"/>
100 <param name="label" value="0.03,0.33"/>
101 <param name="calc" value="canberra"/> 102 <param name="calc" value="canberra"/>
102 <param name="output" value="square"/> 103 <param name="output" value="square"/>
103 <output_collection name="distfiles" count="6"> 104 <output_collection name="distfiles" count="6">
104 <element name="canberra.0.33.square.std" ftype="mothur.dist"> 105 <element name="canberra.0.33.square.std" ftype="mothur.dist">
105 <assert_contents> 106 <assert_contents>
108 </assert_contents> 109 </assert_contents>
109 </element> 110 </element>
110 </output_collection> 111 </output_collection>
111 <expand macro="logfile-test"/> 112 <expand macro="logfile-test"/>
112 </test> 113 </test>
114 <test><!-- test with subsampling with specifying size-->
115 <param name="otu" value="amazon.mothur.shared" ftype="mothur.shared"/>
116 <param name="use" value="yes"/>
117 <param name="subsample" value="2"/>
118 <param name="iters" value="42"/>
119 <param name="label" value="0.10"/>
120 <param name="calc" value="canberra"/>
121 <param name="output" value="square"/>
122 <output_collection name="distfiles" count="3">
123 <element name="canberra.0.10.square.std" ftype="mothur.dist">
124 <assert_contents>
125 <has_text text="forest"/>
126 <has_text text="pasture"/>
127 </assert_contents>
128 </element>
129 </output_collection>
130 <expand macro="logfile-test"/>
131 </test>
113 </tests> 132 </tests>
114 <help> 133 <help><![CDATA[
115 <![CDATA[
116 134
117 @MOTHUR_OVERVIEW@ 135 @MOTHUR_OVERVIEW@
118 136
119 **Command Documentation** 137 **Command Documentation**
120 138
124 .. _shared: https://www.mothur.org/wiki/Shared_file 142 .. _shared: https://www.mothur.org/wiki/Shared_file
125 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared 143 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared
126 144
127 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available. 145 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.
128 146
129 ]]> 147 ]]></help>
130 </help>
131 <expand macro="citations"/> 148 <expand macro="citations"/>
132 </tool> 149 </tool>