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comparison collect.shared.xml @ 0:afac0d63dac6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:13:01 -0400
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children 152f67f91fb6
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-1:000000000000 0:afac0d63dac6
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="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 'collect.shared(
16 shared=otu.dat,
17 #if $label:
18 label=${ str($label).replace(",","-") },
19 #end if
20 #if $calc:
21 calc=${ str($calc).replace(",","-") },
22 #end if
23 #if $groups:
24 groups=${ str($groups).replace(",","-") },
25 #end if
26 freq=$freq,
27 all=true
28 )'
29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur
31 | tee mothur.out.log
32 && rm otu.dat ## don't want this collected into datacollection
33 ]]></command>
34 <inputs>
35 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
36 <param name="label" type="select" multiple="true" label="label - OTU Label filter">
37 <expand macro="labeloptions"/>
38 </param>
39 <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">
40 <options>
41 <filter type="data_meta" ref="otu" key="groups"/>
42 </options>
43 </param>
44 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none are selected)">
45 <expand macro="calc-common"/>
46 <!-- set default option(s) -->
47 <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
48 <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
49 <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</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" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</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="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
55 <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
56 <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
57 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
58 </param>
59 <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"/>
60 </inputs>
61 <outputs>
62 <expand macro="logfile-output"/>
63 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
64 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
65 </collection>
66 </outputs>
67 <tests>
68 <test><!-- test default settings -->
69 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
70 <output_collection name="calcfiles" count="11">
71 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/>
72 </output_collection>
73 <expand macro="logfile-test"/>
74 </test>
75 <test><!-- test with group and label select and all calculators -->
76 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
77 <param name="groups" value="forest,pasture"/>
78 <param name="label" value="0.03,0.05,0.22"/>
79 <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"/>
80 <output_collection name="calcfiles" count="39">
81 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
82 </output_collection>
83 <expand macro="logfile-test"/>
84 </test>
85 </tests>
86 <help>
87 <![CDATA[
88
89 @MOTHUR_OVERVIEW@
90
91 **Command Documentation**
92
93 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: https://www.mothur.org/wiki/Calculators
94
95 .. _calculators: https://www.mothur.org/wiki/Calculators
96 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared
97 ]]>
98 </help>
99 <expand macro="citations"/>
100 </tool>