Mercurial > repos > iuc > mothur_sens_spec

comparison sens.spec.xml @ 2:edde8e7c2946 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 21:54:54 -0400
parents 78776d48bbad
children ddda05cfccb4
comparison
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1:1979ff89fbde 2:edde8e7c2946
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 "$dist" dist.dat && 14 ln -s '$matrix.dist' matrix.dist.dat &&
15 #if str($matrix.method_name.method) == "count" :
16 ln -s '$matrix.method_name.count' matrix.method_name.count.dat &&
17 #else
18 ln -s '$matrix.method_name.names' matrix.method_name.names.dat &&
19 #end if
15 20
16 echo 'sens.spec( 21
17 list=otu.dat, 22 echo 'sens.spec(
18 #if $dist.is_of_type("mothur.dist"): 23 list=otu.dat,
19 column=dist.dat, 24 #if str($matrix.format) == "phylip":
20 #else 25 phylip=matrix.dist.dat,
21 phylip=dist.dat, 26 #else
22 #end if 27 column=matrix.dist.dat,
23 #if $label: 28 #end if
24 label=${ str($label).replace(",","-") }, 29 #if str($matrix.method_name.method) == "count" :
25 #end if 30 count=matrix.method_name.count.dat,
26 precision=$precision, 31 #else
27 cutoff=$cutoff, 32 names=matrix.method_name.names.dat,
28 hard=$hard 33 #end if
29 )' 34 #if $label:
30 | sed 's/ //g' ## mothur trips over whitespace 35 label=${ str($label).replace(",","-") },
31 | mothur 36 #end if
32 | tee mothur.out.log 37 #if $label:
38 label=${ str($label).replace(",","-") },
39 #end if
40 precision=$precision,
41 cutoff=$cutoff
42 )'
43 | sed 's/ //g' ## mothur trips over whitespace
44 | mothur
45 | tee mothur.out.log
33 ]]></command> 46 ]]></command>
34 <inputs> 47 <inputs>
48 <conditional name="matrix">
49 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
50 <option value="column">Pairwise Column Matrix </option>
51 <option value="phylip">Phylip Distance Matrix</option>
52 </param>
53 <when value="column">
54 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
55 <conditional name="method_name">
56 <param name="method" type="select" label="Select a Method" help="">
57 <option value="count">count file associated with your distance matrix.</option>
58 <option value="name">name file associated with your distance matrix. </option>
59 </param>
60 <when value="count">
61 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
62 </when>
63 <when value="name">
64 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
65 </when>
66
67 </conditional>
68 </when>
69 <when value="phylip">
70 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
71 </when>
72 </conditional>
35 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> 73 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
36 <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/> 74 <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/>
37 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made."> 75 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
38 <options> 76 <options>
39 <filter type="data_meta" ref="otu" key="labels"/> 77 <filter type="data_meta" ref="otu" key="labels"/>
40 </options> 78 </options>
41 </param> 79 </param>
42 <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/> 80 <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/>
43 <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> 81 <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
44 <param name="hard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/> 82 <expand macro="param-savelog"/>
45 </inputs> 83 </inputs>
46 <outputs> 84 <outputs>
47 <expand macro="logfile-output"/> 85 <expand macro="logfile-output"/>
48 <data name="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/> 86 <data name="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/>
49 </outputs> 87 </outputs>
50 <tests> 88 <tests>
51 <test> 89 <test>
52 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 90 <param name="count" value="amazon.count_table"/>
91 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
53 <param name="dist" value="amazon.dist" ftype="mothur.dist"/> 92 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
54 <output name="sensspec" md5="5eb92a89c4e1fd78c10e5bbe55ee2a7a" ftype="tabular"/> 93 <output name="sensspec" md5="720789a7ef4da26928a61161279d7344" ftype="tabular"/>
94 <param name="savelog" value="true"/>
55 <expand macro="logfile-test"/> 95 <expand macro="logfile-test"/>
56 </test> 96 </test>
57 <test> 97 <test>
98 <param name="count" value="amazon.count_table"/>
99 <param name="names" value="amazon.names"/>
58 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> 100 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
59 <param name="dist" value="amazon.dist" ftype="mothur.dist"/> 101 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
60 <param name="cutoff" value="0.10"/> 102 <param name="cutoff" value="0.10"/>
61 <param name="label" value="0.03,0.05,0.22"/> 103 <param name="label" value="0.03,0.05,0.22"/>
62 <output name="sensspec" md5="8e2f46ef59b1ac097a9de2e0ab669bb2" ftype="tabular"/> 104 <output name="sensspec" md5="3992dec1d799ec3a061b3ef713a58382" ftype="tabular"/>
105 <param name="savelog" value="true"/>
63 <expand macro="logfile-test"/> 106 <expand macro="logfile-test"/>
64 </test> 107 </test>
65 </tests> 108 </tests>
66 <help> 109 <help><![CDATA[
67 <![CDATA[
68 110
69 @MOTHUR_OVERVIEW@ 111 @MOTHUR_OVERVIEW@
70 112
71 **Command Documentation** 113 **Command Documentation**
72 114
75 117
76 .. _list: https://www.mothur.org/wiki/List_file 118 .. _list: https://www.mothur.org/wiki/List_file
77 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix 119 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
78 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix 120 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
79 .. _sens.spec: https://www.mothur.org/wiki/Sens.spec 121 .. _sens.spec: https://www.mothur.org/wiki/Sens.spec
80 ]]> 122
81 </help> 123 ]]></help>
82 <expand macro="citations"/> 124 <expand macro="citations"/>
83 </tool> 125 </tool>