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comparison community.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="community" name="Community" version="0.0.16">
2 <description>'Community' Data Input</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">community.R
8 #if str($CountsFile).strip() != "":
9 --CountsFile="$CountsFile"
10 #end if
11 #if str($SamplesFile).strip() != "":
12 --SamplesFile="$SamplesFile"
13 #end if
14 #if str($K).strip() != "":
15 --K="$K"
16 #end if
17 #if str($A).strip() != "":
18 --A="$A"
19 #end if
20 #if str($Transform).strip() != "":
21 --Transform="$Transform"
22 #end if
23 #if str($SampleName).strip() != "":
24 --SampleName="$SampleName"
25 #end if
26 #if str($ColumnClasses).strip() != "":
27 --ColumnClasses="$ColumnClasses"
28 #end if
29 #if str($OutputFile).strip() != "":
30 --OutputFile="$OutputFile"
31 #end if
32
33 2&gt;&amp;1</command>
34 <inputs>
35 <param optional="false" name="CountsFile" type="data" help="Name of a CSV file containing OTU samples." label="[required] Counts File">
36 <validator type="empty_field" message="This field is required."/>
37 </param>
38 <param optional="false" name="SamplesFile" type="data" help="Name of a CSV file containing sample data." label="[required] Samples File">
39 <validator type="empty_field" message="This field is required."/>
40 </param>
41 <param optional="true" name="K" type="float" value="0" help="The parameters 'K' and 'A' together define a 'K over A'&#10;filter. The filter can be used to include only some taxa. The&#10;idea is that a taxonomic entity is only included if at least&#10;'A' reads are present in at least 'K' samples. The default is&#10;A = K = 0, i.e., include all taxa. Specify 'K' in the box&#10;above." label="K">
42 <validator type="empty_field" message="This field is required."/>
43 </param>
44 <param optional="true" name="A" type="float" value="0" help="Include only taxa with at least K samples greater than A, as&#10;described for the parameter K." label="A">
45 <validator type="empty_field" message="This field is required."/>
46 </param>
47 <param optional="true" name="Transform" type="select" help="(Optional) A transformation applied to all count data, after&#10;the 'K Over A' filter has been run. Possible values include&#10;&quot;log&quot; (actually, log(x + .5) to avoid logarithms of zero&#10;counts) and &quot;asinh&quot; (inverse hyperboloic sine, a log-like&#10;transformation with better behavior near zero)." label="Transform" force_select="FALSE">
48 <validator type="empty_field" message="This field is required."/>
49 <option value="none">none</option>
50 <option value="log">log</option>
51 <option value="asinh">asinh</option>
52 </param>
53 <param optional="true" name="SampleName" type="text" help="(Optional) Samples File column name containing names by&#10;which samples are identified in all subsequent calculations.&#10;If two rows have the same Sample Name, then corresponding&#10;counts in the Counts File are added together." size="60" label="Sample Name">
54 <validator type="empty_field" message="This field is required."/>
55 </param>
56 <param optional="true" name="ColumnClasses" type="text" help="(Optional) Comma-separated names specifying how each&#10;column is to be represented. There must be as many names, and&#10;in the same order, as there are columns in the file. Typical&#10;values include: logical, integer, numeric, character, factor,&#10;Date. Use 'factor' to indicate a variable with discrete&#10;levels, e.g., sex (with levels Male, Female) tissue type&#10;(with levels Tumor, Normal), etc. When 'Date' is used, dates&#10;should be formatted consistently as year-month-day or&#10;year/month/day, e.g., 2014-03-26; poorly formed dates will be&#10;converted to 'NA' values." size="60" label="Column Classes">
57 <validator type="empty_field" message="This field is required."/>
58 </param>
59 </inputs>
60 <outputs>
61 <data format="rda" name="OutputFile" label="community.rda"/>
62 </outputs>
63 <help>
64 **Description**
65
66 Input a CSV file of integer-valued counts of each taxon (row) in
67 each sample (column), and a CSV file of annotations on each
68 sample. The result is used in down-stream analysis.
69 </help>
70 </tool>