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comparison cooccurrence.xml @ 0:12b4f093e6c4 draft default tip

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planemo upload commit 2774930eebe258ecd56c8f1c5ddabf5092282ab9
author bcclaywell
date Mon, 12 Oct 2015 16:46:15 -0400
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-1:000000000000 0:12b4f093e6c4
1 <tool id="cooccurrence" name="Cooccurrence" version="0.0.16">
2 <description>Taxonomic Co-occurrence Heatmap</description>
3 <requirements>
4 <requirement type="package" version="3.1.2">R</requirement>
5 <requirement type="package" version="2014-05-02">microbiome_community</requirement>
6 </requirements>
7 <command interpreter="Rscript --vanilla">cooccurrence.R
8 #if str($CommunityFile).strip() != "":
9 --CommunityFile="$CommunityFile"
10 #end if
11 #if str($TaxonQuantile).strip() != "":
12 --TaxonQuantile="$TaxonQuantile"
13 #end if
14 #if str($Transform).strip() != "":
15 --Transform="$Transform"
16 #end if
17 #if str($OutputFile).strip() != "":
18 --OutputFile="$OutputFile"
19 #end if
20
21 2&gt;&amp;1</command>
22 <inputs>
23 <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function." label="[required] Community File">
24 <validator type="empty_field" message="This field is required."/>
25 </param>
26 <param optional="true" name="TaxonQuantile" type="float" value="0" help="(Optional, default 0) Numeric value between 0 and 1,&#10;limiting only taxa more frequent than the specified quantile." label="Taxon Quantile">
27 <validator type="empty_field" message="This field is required."/>
28 </param>
29 <param optional="true" name="Transform" type="select" help="(Optional; default 'none') Character string defining how&#10;count data are to be transformed prior to calculation of&#10;co-occurrence. Possible values are 'none', 'log1' (log of 1 +&#10;the observed count, to allow for zeros in the data), 'asinh'&#10;(a log-like transformation that handles zeros more&#10;naturally), 'sqrt' (square root, a transformation commonly&#10;used for count data)." label="Transform" force_select="FALSE">
30 <validator type="empty_field" message="This field is required."/>
31 <option value="none">none</option>
32 <option value="log1">log1</option>
33 <option value="asinh">asinh</option>
34 <option value="sqrt">sqrt</option>
35 </param>
36 </inputs>
37 <outputs>
38 <data format="pdf" name="OutputFile" label="cooccurrence.pdf"/>
39 </outputs>
40 <help>
41 **Description**
42
43 Taxonomic co-occurrence across samples, displayed as a heatmap.
44 </help>
45 </tool>