Mercurial > repos > iuc > mothur_dist_shared

comparison dist.shared.xml @ 0:7773b7afb53d 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 a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:20:24 -0400
parents
children b7da1494afa1
comparison
equal deleted inserted replaced
-1:000000000000 0:7773b7afb53d
1 <tool profile="16.07" id="mothur_dist_shared" name="Dist.shared" version="@WRAPPER_VERSION@.0">
2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat &&
14
15 echo 'dist.shared(
16 shared=otu.dat,
17 #if $label:
18 label=${ str($label).replace(",","-") },
19 #end if
20 #if $groups:
21 groups=${ str($groups).replace(",","-") },
22 #end if
23 #if $calc:
24 calc=${ str($calc).replace(",","-") },
25 #end if
26 #if $subsampling.use == "yes":
27 #if $subsampling.subsample:
28 subsample=$subsampling.subsample,
29 #end if
30 iters=$subsampling.iters,
31 #end if
32 output=$output,
33 processors='\${GALAXY_SLOTS:-8}'
34 )'
35 | sed 's/ //g' ## mothur trips over whitespace
36 | mothur
37 | tee mothur.out.log
38 ]]></command>
39 <inputs>
40 <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">
42 <expand macro="labeloptions"/>
43 </param>
44 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
45 <options>
46 <filter type="data_meta" ref="otu" key="groups"/>
47 </options>
48 </param>
49 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
50 <expand macro="calc-common"/>
51 <!-- set default option(s) -->
52 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
53 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
54 </param>
55 <conditional name="subsampling">
56 <param name="use" type="select" label="subsample">
57 <option value="no" selected="true">no</option>
58 <option value="yes">yes</option>
59 </param>
60 <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"/>
62 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
63 </when>
64 <when value="no"/>
65 </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">
67 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
68 <option value="square">Phylip formatted Square Matrix</option>
69 </param>
70 </inputs>
71 <outputs>
72 <expand macro="logfile-output"/>
73 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files">
74 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"/>
75 </collection>
76 </outputs>
77 <tests>
78 <test><!-- test with defaults -->
79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
80 <output_collection name="distfiles" count="72">
81 <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
82 </output_collection>
83 <expand macro="logfile-test"/>
84 </test>
85 <test><!-- test with label,group select and all calculators -->
86 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
87 <param name="label" value="0.05,0.22"/>
88 <param name="groups" value="forest,pasture"/>
89 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structeuclidean,structpearson,sharednseqs,sharedobserved"/>
90 <output_collection name="distfiles" count="74">
91 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
92 </output_collection>
93 <expand macro="logfile-test"/>
94 </test>
95 <test><!-- test with subsampling -->
96 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
97 <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="output" value="square"/>
103 <output_collection name="distfiles" count="6">
104 <element name="canberra.0.33.square.std" ftype="mothur.dist">
105 <assert_contents>
106 <has_text text="forest"/>
107 <has_text text="pasture"/>
108 </assert_contents>
109 </element>
110 </output_collection>
111 <expand macro="logfile-test"/>
112 </test>
113 </tests>
114 <help>
115 <![CDATA[
116
117 @MOTHUR_OVERVIEW@
118
119 **Command Documentation**
120
121 The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
122
123 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
124 .. _shared: https://www.mothur.org/wiki/Shared_file
125 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared
126
127 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.
128
129 ]]>
130 </help>
131 <expand macro="citations"/>
132 </tool>