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comparison reducedDimensionality.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="reducedDimensionality" name="Reduced Dimensionality" version="0.0.16">
2 <description>Taxnomic Dimensionality Reduction (Ordination) Plot</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">reducedDimensionality.R
8 #if str($CommunityFile).strip() != "":
9 --CommunityFile="$CommunityFile"
10 #end if
11 #if str($Attributes).strip() != "":
12 --Attributes="$Attributes"
13 #end if
14 #if str($OrdinationAlgorithm).strip() != "":
15 --OrdinationAlgorithm="$OrdinationAlgorithm"
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="Attributes" type="text" help="Comma-separated names of SamplesFile columns on which&#10;ribbons are to be plotted. Samples are ordered by the first&#10;element of Attributes; Attributes must identify more than 1&#10;SampleFile column. Example: Nugent_3_group, Amsel,&#10;Nugent_Lactobacillus, pH, Clue" size="60" label="Attributes">
27 <validator type="empty_field" message="This field is required."/>
28 </param>
29 <param optional="true" name="OrdinationAlgorithm" type="select" value="MDS" help="Algorithm to use for oridination &quot;PCoA&quot; (Principle&#10;Coordinates Analysis), &quot;NMDS&quot; (Non-Metric Multidimensional&#10;Scaling), &quot;CA&quot; (Correspondence Analysis), &quot;DPCoA&quot; (Double&#10;Principle Components Analysis)." label="Ordination Algorithm" force_select="FALSE">
30 <validator type="empty_field" message="This field is required."/>
31 <option value="MDS">MDS</option>
32 </param>
33 </inputs>
34 <outputs>
35 <data format="pdf" name="OutputFile" label="reducedDimensionality.pdf"/>
36 </outputs>
37 <help>
38 **Description**
39
40 Reduce dimensionality of taxonomic abundance.
41 </help>
42 </tool>