Mercurial > repos > iuc > mothur_collect_shared

comparison collect.shared.xml @ 3:c46d135d6a32 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 10:12:35 -0500
parents 0bb0ddd83eff
children c6684441526a
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2:1361cd29d2ef 3:c46d135d6a32
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"/>
60 </inputs> 61 </inputs>
61 <outputs> 62 <outputs>
62 <expand macro="logfile-output"/> 63 <expand macro="logfile-output"/>
63 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators"> 64 <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
64 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/> 65 <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
81 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/> 82 <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
82 </output_collection> 83 </output_collection>
83 <expand macro="logfile-test"/> 84 <expand macro="logfile-test"/>
84 </test> 85 </test>
85 </tests> 86 </tests>
86 <help> 87 <help><![CDATA[
87 <![CDATA[
88 88
89 @MOTHUR_OVERVIEW@ 89 @MOTHUR_OVERVIEW@
90 90
91 **Command Documentation** 91 **Command Documentation**
92 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 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 94
95 .. _calculators: https://www.mothur.org/wiki/Calculators 95 .. _calculators: https://www.mothur.org/wiki/Calculators
96 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared 96 .. _collect.shared: https://www.mothur.org/wiki/Collect.shared
97 ]]> 97
98 </help> 98 ]]></help>
99 <expand macro="citations"/> 99 <expand macro="citations"/>
100 </tool> 100 </tool>