Mercurial > repos > iuc > mothur_collect_shared

comparison collect.shared.xml @ 2:152f67f91fb6 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 22:06:36 -0400
parents afac0d63dac6
children 9c78c5ffa049
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1:fd3fedbebdab 2:152f67f91fb6
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 14
15 echo 'collect.shared( 15 echo 'collect.shared(
16 shared=otu.dat, 16 shared=otu.dat,
17 #if $label: 17 #if $label:
18 label=${ str($label).replace(",","-") }, 18 label=${ str($label).replace(",","-") },
19 #end if 19 #end if
20 #if $calc: 20 #if $calc:
21 calc=${ str($calc).replace(",","-") }, 21 calc=${ str($calc).replace(",","-") },
22 #end if 22 #end if
23 #if $groups: 23 #if $groups:
24 groups=${ str($groups).replace(",","-") }, 24 groups=${ str($groups).replace(",","-") },
25 #end if 25 #end if
26 freq=$freq, 26 freq=$freq,
27 all=true 27 all=true
28 )' 28 )'
29 | sed 's/ //g' ## mothur trips over whitespace 29 | sed 's/ //g' ## mothur trips over whitespace
30 | mothur 30 | mothur
31 | tee mothur.out.log 31 | tee mothur.out.log
32 && rm otu.dat ## don't want this collected into datacollection 32 && rm otu.dat ## don't want this collected into datacollection
33 ]]></command> 33 ]]></command>
34 <inputs> 34 <inputs>
35 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 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"> 36 <param name="label" type="select" multiple="true" label="label - OTU Label filter">
37 <expand macro="labeloptions"/> 37 <expand macro="labeloptions"/>
54 <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</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> 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> 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> 57 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
58 </param> 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"/> 59 <param name="freq" type="float" value="100" label="freq - indicates when to output your data"
60 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"/>
61 <expand macro="param-savelog"/>
60 </inputs> 62 </inputs>
61 <outputs> 63 <outputs>
62 <expand macro="logfile-output"/> 64 <expand macro="logfile-output"/>
63 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators"> 65 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
64 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/> 66 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
68 <test><!-- test default settings --> 70 <test><!-- test default settings -->
69 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 71 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
70 <output_collection name="calcfiles" count="11"> 72 <output_collection name="calcfiles" count="11">
71 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/> 73 <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/>
72 </output_collection> 74 </output_collection>
75 <param name="savelog" value="true"/>
73 <expand macro="logfile-test"/> 76 <expand macro="logfile-test"/>
74 </test> 77 </test>
75 <test><!-- test with group and label select and all calculators --> 78 <test><!-- test with group and label select and all calculators -->
76 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
77 <param name="groups" value="forest,pasture"/> 80 <param name="groups" value="forest,pasture"/>
78 <param name="label" value="0.03,0.05,0.22"/> 81 <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"/> 82 <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"> 83 <output_collection name="calcfiles" count="39">
81 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/> 84 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
82 </output_collection> 85 </output_collection>
86 <param name="savelog" value="true"/>
83 <expand macro="logfile-test"/> 87 <expand macro="logfile-test"/>
84 </test> 88 </test>
85 </tests> 89 </tests>
86 <help> 90 <help><![CDATA[
87 <![CDATA[
88 91
89 @MOTHUR_OVERVIEW@ 92 @MOTHUR_OVERVIEW@
90 93
91 **Command Documentation** 94 **Command Documentation**
92 95
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 96 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 97
95 .. _calculators: https://www.mothur.org/wiki/Calculators 98 .. _calculators: https://www.mothur.org/wiki/Calculators
96 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared 99 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared
97 ]]> 100
98 </help> 101 ]]></help>
99 <expand macro="citations"/> 102 <expand macro="citations"/>
100 </tool> 103 </tool>