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Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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e5c3175506b7 Initial tool configs for qiime, most need work.
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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_tmpdir='$__new_file_path__'
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9 make_rarefaction_plots.py
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10 --input_dir=$input_dir
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11 --map_fname=$map_fname
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12 --colorby=$colorby
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13 --prefs_path=$prefs_path
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14 --background_color=$background_color
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15 --imagetype=$imagetype
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16 --resolution=$resolution
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17 --ymax=$ymax
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18 $webpage
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19 --output_dir=$__new_file_path__
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20 </command>
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21 <inputs>
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22 <param name="input_dir" type="text" label="input_dir"
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23 help="name of folder containing rarefaction files, takes output from collate_alpha.py. The user can also supply a list of files, which are comma-separated. [REQUIRED]"/>
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24 <param name="map_fname" type="data" format="tabular" label="map_fname"
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25 help="name of mapping file [REQUIRED]"/>
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26 <param name="colorby" type="text" label="colorby"
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27 help="name of columns to make rarefaction graphs of, comma delimited no spaces."/>
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28 <param name="prefs_path" type="text" label="prefs_path"
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29 help="preferences file for coloring of columns."/>
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30 <param name="background_color" type="text" value="white" label="background_color"
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31 help="Background color for graphs."/>
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32 <param name="imagetype" type="text" value="png" label="imagetype"
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33 help="extension for image type choose from (png, svg, pdf). WARNING: Some formats may not properly open in your browser! [default: png]"/>
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34 <param name="resolution" type="integer" value="75" label="resolution"
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35 help="output image resolution, [default: 75]"/>
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36 <param name="ymax" type="integer" value="-1" label="ymax"
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37 help="this is the ymax value to be used for the plots, so you can compare rarefaction plots between two different analyses [default: ('NO', 'DEFAULT')]"/>
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38 <param name="webpage" type="boolean" truevalue="" falsevalue="--webpage" checked="false" label="webpage"
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39 help="this is allows to user to not create the webpage, which may be slow with large datasets [default: True]"/>
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40 </inputs>
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41 <outputs>
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42
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43 </outputs>
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44 <tests>
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45 </tests>
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46 <help>
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47
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48 </help>
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49 </tool>
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50