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annotate 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 <tool id="community" name="Community" version="0.0.16">
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2 <description>'Community' Data Input</description>
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3 <requirements>
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4 <requirement type="package" version="3.1.2">R</requirement>
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5 <requirement type="package" version="2014-05-02">microbiome_community</requirement>
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6 </requirements>
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7 <command interpreter="Rscript --vanilla">community.R
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8 #if str($CountsFile).strip() != "":
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9 --CountsFile="$CountsFile"
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10 #end if
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11 #if str($SamplesFile).strip() != "":
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12 --SamplesFile="$SamplesFile"
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13 #end if
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14 #if str($K).strip() != "":
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15 --K="$K"
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16 #end if
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17 #if str($A).strip() != "":
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18 --A="$A"
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19 #end if
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20 #if str($Transform).strip() != "":
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21 --Transform="$Transform"
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22 #end if
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23 #if str($SampleName).strip() != "":
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24 --SampleName="$SampleName"
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25 #end if
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26 #if str($ColumnClasses).strip() != "":
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27 --ColumnClasses="$ColumnClasses"
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28 #end if
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29 #if str($OutputFile).strip() != "":
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30 --OutputFile="$OutputFile"
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31 #end if
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32
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33 2&gt;&amp;1</command>
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34 <inputs>
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35 <param optional="false" name="CountsFile" type="data" help="Name of a CSV file containing OTU samples." label="[required] Counts File">
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36 <validator type="empty_field" message="This field is required."/>
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37 </param>
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38 <param optional="false" name="SamplesFile" type="data" help="Name of a CSV file containing sample data." label="[required] Samples File">
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39 <validator type="empty_field" message="This field is required."/>
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40 </param>
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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">
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42 <validator type="empty_field" message="This field is required."/>
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43 </param>
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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">
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45 <validator type="empty_field" message="This field is required."/>
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46 </param>
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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">
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48 <validator type="empty_field" message="This field is required."/>
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49 <option value="none">none</option>
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50 <option value="log">log</option>
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51 <option value="asinh">asinh</option>
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52 </param>
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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">
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54 <validator type="empty_field" message="This field is required."/>
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55 </param>
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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">
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57 <validator type="empty_field" message="This field is required."/>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data format="rda" name="OutputFile" label="community.rda"/>
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62 </outputs>
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63 <help>
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64 **Description**
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65
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66 Input a CSV file of integer-valued counts of each taxon (row) in
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67 each sample (column), and a CSV file of annotations on each
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68 sample. The result is used in down-stream analysis.
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69 </help>
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70 </tool>