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comparison collect.shared.xml @ 0:e9f8b81fa72c 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 16:26:58 -0400
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-1:000000000000 0:e9f8b81fa72c
1 <tool profile="16.07" id="mothur_collect_shared" name="Collect.shared" version="@WRAPPER_VERSION@.0">
2 <description>Generate collector's curves for calculators on OTUs</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 'collect.shared(
13 shared=otu.dat,
14 #if $label:
15 label=${ str($label).replace(",","-") },
16 #end if
17 #if $calc:
18 calc=${ str($calc).replace(",","-") },
19 #end if
20 #if $groups:
21 groups=${ str($groups).replace(",","-") },
22 #end if
23 freq=$freq,
24 all=true
25 )'
26 | sed 's/ //g' ## mothur trips over whitespace
27 | mothur
28 && rm otu.dat ## don't want this collected into datacollection
29 ]]></command>
30 <inputs>
31 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
32 <param name="label" type="select" multiple="true" label="label - OTU Label filter">
33 <expand macro="labeloptions"/>
34 </param>
35 <param name="groups" type="select" multiple="true" label="groups - Groups filter (uses all groups if none are selected)" help="To filter: select select at least 2 groups">
36 <options>
37 <filter type="data_meta" ref="otu" key="groups"/>
38 </options>
39 </param>
40 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none are selected)">
41 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
42 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
43 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
44 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
45 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
46 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
47 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
48 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
49 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
50 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
51 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
52 <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
53 <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
54 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
55 <option value="hamming">hamming - Community Membership Similarity -</option>
56 <option value="memchi2">memchi2 - Community Membership Similarity -</option>
57 <option value="memchord">memchord - Community Membership Similarity -</option>
58 <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
59 <option value="mempearson">mempearson - Community Membership Similarity -</option>
60 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
61 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
62 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
63 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
64 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
65 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
66 <option value="canberra">canberra - Community Structure Similarity -</option>
67 <option value="gower">gower - Community Structure Similarity -</option>
68 <option value="hellinger">hellinger - Community Structure Similarity -</option>
69 <option value="manhattan">manhattan - Community Structure Similarity -</option>
70 <option value="odum">odum - Community Structure Similarity -</option>
71 <option value="soergel">soergel - Community Structure Similarity -</option>
72 <option value="spearman">spearman - Community Structure Similarity -</option>
73 <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
74 <option value="structchi2">structchi2 - Community Structure Similarity -</option>
75 <option value="structchord">structchord - Community Structure Similarity -</option>
76 <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
77 <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
78 <option value="structpearson">structpearson - Community Structure Similarity -</option>
79 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
80 </param>
81 <param name="freq" type="float" value="100" label="freq - indicates when to output your data" help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
82 </inputs>
83 <outputs>
84 <expand macro="logfile-output"/>
85 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
86 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
87 </collection>
88 </outputs>
89 <tests>
90 <test><!-- test default settings -->
91 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
92 <output_collection name="calcfiles" count="11">
93 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/>
94 </output_collection>
95 <expand macro="logfile-test"/>
96 </test>
97 <test><!-- test with group and label select and all calculators -->
98 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
99 <param name="groups" value="forest,pasture"/>
100 <param name="label" value="0.03,0.05,0.22"/>
101 <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,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs"/>
102 <output_collection name="calcfiles" count="39">
103 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
104 </output_collection>
105 <expand macro="logfile-test"/>
106 </test>
107 </tests>
108 <help>
109 <![CDATA[
110
111 @MOTHUR_OVERVIEW@
112
113 **Command Documenation**
114
115 The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
116
117 .. _calculators: http://www.mothur.org/wiki/Calculators
118 .. _collect.shared: http://www.mothur.org/wiki/Collect.shared
119 ]]>
120 </help>
121 <expand macro="citations"/>
122 </tool>