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1 <tool id="make_rarefaction_plots" name="make_rarefaction_plots" version="1.2.0">
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2 <description>Generate Rarefaction Plots</description>
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3 <requirements>
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4 <requirement type="binary">make_rarefaction_plots.py</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 qiime_wrapper.py
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8 --galaxy_datasets='^\S+\.html$:'$plot
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9 --galaxy_outputdir=$plot.extra_files_path
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10 make_rarefaction_plots.py
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11 --input_dir=$input_dir.extra_files_path
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12 --map_fname=$map_fname
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13 #if $colorby != None and $colorby.__str__ != 'None' and len($colorby.__str__) > 0:
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14 --colorby=$colorby
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15 #end if
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16 #if $prefs_path != None and $prefs_path.__str__ != 'None':
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17 --prefs_path=$prefs_path
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18 #end if
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19 #if $ymax != None and $ymax.__str__ != '':
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20 --ymax=$ymax
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21 #end if
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22 --background_color=$background_color
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23 --imagetype=$imagetype
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24 --resolution=$resolution
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25 --output_dir=$plot.extra_files_path
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26 </command>
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27 <inputs>
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28 <param name="input_dir" type="data" format="txt" label="input_dir" help="Rarefaction file (I.E. log output from collate_alpha). [REQUIRED]"/>
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29 <param name="map_fname" type="data" format="tabular" label="map_fname" help="Name of mapping file [REQUIRED]"/>
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30 <param name="colorby" type="text" label="colorby" help="Name of columns to make rarefaction graphs of, comma delimited, no spaces. [OPTIONAL]"/>
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31 <param name="prefs_path" type="data" format="txt" optional="true" label="prefs_path" help="Preferences file for coloring of columns. [OPTIONAL]"/>
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32 <param name="background_color" type="select" value="white" label="background_color" help="Background color for graphs. [default: white]">
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33 <option value="white" selected="true">White</option>
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34 <option value="black">Black</option>
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35 </param>
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36 <param name="imagetype" type="select" label="Image Type"
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37 help="Type of image to produce (i.e. pdf,svg,png). [default: png]">
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38 <option value="pdf">pdf</option>
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39 <option value="svg">svg</option>
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40 <option value="png" selected="true">png</option>
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41 </param>
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42 <param name="resolution" type="integer" value="75" label="resolution"
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43 help="output image resolution, [default: 75]"/>
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44 <param name="ymax" type="text" label="ymax"
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45 help="this is the ymax value to be used for the plots, so you can compare rarefaction plots between two different analyses [default: none]"/>
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46 </inputs>
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47 <outputs>
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48 <data format="html" name="plot" label="${tool.name} on ${on_string}"/>
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49 </outputs>
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50 <tests>
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51 </tests>
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52 <help>This tool takes the log file output from collate_alpha to create an html file of rarefaction plots wherein you can plot by sample and/or by category.
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53
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54 For more information, see make_rarefaction_plots_ in the Qiime documentation.
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55
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56 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
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57
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58 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
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59
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60 .. _make_rarefaction_plots: http://qiime.org/scripts/make_rarefaction_plots.html</help>
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61 </tool>
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62
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