Mercurial > repos > bcclaywell > microbiome_community_suite

comparison presenceAbsence.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="presenceAbsence" name="Presence Absence" version="0.0.16">
2 <description>Taxonomic Presence / Absence Summary and Chi-squared Test</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">presenceAbsence.R
8 #if str($CommunityFile).strip() != "":
9 --CommunityFile="$CommunityFile"
10 #end if
11 #if str($Attribute).strip() != "":
12 --Attribute="$Attribute"
13 #end if
14 #if str($OutputFile).strip() != "":
15 --OutputFile="$OutputFile"
16 #end if
17
18 2&gt;&amp;1</command>
19 <inputs>
20 <param optional="false" name="CommunityFile" format="rda" type="data" help="File created by the 'community' function" label="[required] Community File">
21 <validator type="empty_field" message="This field is required."/>
22 </param>
23 <param optional="true" name="Attribute" type="text" help="Name of a sample attribute to summarize presence / absence&#10;data. Example: Nugent_2_group" size="60" label="Attribute">
24 <validator type="empty_field" message="This field is required."/>
25 </param>
26 </inputs>
27 <outputs>
28 <data format="csv" name="OutputFile" label="presenceAbsence.csv"/>
29 </outputs>
30 <help>
31 **Description**
32
33 Summarize samples with each taxon present, grouped by factor
34 </help>
35 </tool>