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comparison dist.shared.xml @ 0:e478ba802667 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:30:09 -0400
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children 566e0fba8f4b
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-1:000000000000 0:e478ba802667
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11
12 echo 'dist.shared(
13 shared=otu.dat,
14 #if $label:
15 label=${ str($label).replace(",","-") },
16 #end if
17 #if $groups:
18 groups=${ str($groups).replace(",","-") },
19 #end if
20 #if $calc:
21 calc=${ str($calc).replace(",","-") },
22 #end if
23 #if $subsampling.use == "yes":
24 #if $subsampling.subsample:
25 subsample=$subsampling.subsample,
26 #end if
27 iters=$subsampling.iters,
28 #end if
29 output=$output,
30 processors='\${GALAXY_SLOTS:-8}'
31 )'
32 | sed 's/ //g' ## mothur trips over whitespace
33 | mothur
34 ]]></command>
35 <inputs>
36 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
37 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true">
38 <expand macro="labeloptions"/>
39 </param>
40 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
41 <options>
42 <filter type="data_meta" ref="otu" key="groups"/>
43 </options>
44 </param>
45 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
46 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
47 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
48 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
49 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
50 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
51 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
52 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
53 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
54 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
55 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
56 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
57 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
58 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
59 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
60 <option value="hamming">hamming - Community Membership Similarity -</option>
61 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
62 <option value="memchord">memchord - Community Membership Similarity -</option>
63 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
64 <option value="mempearson">mempearson - Community Membership Similarity -</option>
65 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
66 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
67 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
68 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
69 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
70 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
71 <option value="canberra">canberra - Community Structure Similarity -</option>
72 <option value="gower">gower - Community Structure Similarity -</option>
73 <option value="hellinger">hellinger - Community Structure Similarity -</option>
74 <option value="manhattan">manhattan - Community Structure Similarity -</option>
75 <option value="odum">odum - Community Structure Similarity -</option>
76 <option value="soergel">soergel - Community Structure Similarity -</option>
77 <option value="spearman">spearman - Community Structure Similarity -</option>
78 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
79 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
80 <option value="structchord">structchord - Community Structure Similarity -</option>
81 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
82 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
83 <option value="structpearson">structpearson - Community Structure Similarity -</option>
84 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
85 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
86 </param>
87 <conditional name="subsampling">
88 <param name="use" type="select" label="subsample">
89 <option value="no" selected="true">no</option>
90 <option value="yes">yes</option>
91 </param>
92 <when value="yes">
93 <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"/>
94 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
95 </when>
96 <when value="no"/>
97 </conditional>
98 <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
99 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
100 <option value="square">Phylip formatted Square Matrix</option>
101 </param>
102 </inputs>
103 <outputs>
104 <expand macro="logfile-output"/>
105 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files">
106 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"/>
107 </collection>
108 </outputs>
109 <tests>
110 <test><!-- test with defaults -->
111 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
112 <output_collection name="distfiles" count="72">
113 <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
114 </output_collection>
115 <expand macro="logfile-test"/>
116 </test>
117 <test><!-- test with label,group select and all calculators -->
118 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
119 <param name="label" value="0.05,0.22"/>
120 <param name="groups" value="forest,pasture"/>
121 <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"/>
122 <output_collection name="distfiles" count="74">
123 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
124 </output_collection>
125 <expand macro="logfile-test"/>
126 </test>
127 <test><!-- test with subsampling -->
128 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
129 <param name="use" value="yes"/>
130 <param name="subsample" value="10"/>
131 <param name="iters" value="42"/>
132 <param name="label" value="0.03,0.33"/>
133 <param name="calc" value="canberra"/>
134 <param name="output" value="square"/>
135 <output_collection name="distfiles" count="6">
136 <element name="canberra.0.33.square.std" ftype="mothur.dist">
137 <assert_contents>
138 <has_text text="forest"/>
139 <has_text text="pasture"/>
140 </assert_contents>
141 </element>
142 </output_collection>
143 <expand macro="logfile-test"/>
144 </test>
145 </tests>
146 <help>
147 <![CDATA[
148
149 @MOTHUR_OVERVIEW@
150
151 **Command Documenation**
152
153 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: http://www.mothur.org/wiki/Calculators
154
155 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
156 .. _shared: http://www.mothur.org/wiki/Shared_file
157 .. _dist.shared: http://www.mothur.org/wiki/Dist.shared
158
159 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.
160
161 ]]>
162 </help>
163 <expand macro="citations"/>
164 </tool>