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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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1 <tool id="make_distance_histograms" name="make_distance_histograms" version="1.2.0">
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2 <description>Make distance histograms</description>
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3 <requirements>
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4 <requirement type="binary">make_distance_histograms.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='$__new_file_path__'
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9 make_distance_histograms.py
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10 --distance_matrix_file=$distance_matrix_file
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11 --map_fname=$map_fname
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12 --prefs_path=$prefs_path
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13 --dir_path=$dir_path
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14 --background_color=$background_color
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15 $monte_carlo
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16 $suppress_html_output
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17 --fields=$fields
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18 --monte_carlo_iters=$monte_carlo_iters
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19 </command>
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20 <inputs>
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21 <param name="distance_matrix_file" type="data" format="txt" label="distance_matrix_file"
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22 help="Path to distance matrix file. [REQUIRED]"/>
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23 <param name="map_fname" type="data" format="tabular" label="map_fname"
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24 help="This is the metadata mapping file [default=('NO', 'DEFAULT')] [REQUIRED]"/>
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25 <param name="prefs_path" type="text" label="prefs_path"
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26 help="This is the user-generated preferences file. NOTE: This is a file with a dictionary containing preferences for the analysis. This dict must have a 'Fields' key mapping to a list of desired fields. [default: ('NO', 'DEFAULT')]"/>
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27 <param name="dir_path" type="text" value="." label="dir_path"
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28 help="Directory to output data for all analyses. [default: .]"/>
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29 <param name="background_color" type="text" value="white" label="background_color"
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30 help="This is the background color to use in the plots (Options are 'black' or 'white'. [default: white]"/>
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31 <param name="monte_carlo" type="boolean" truevalue="--monte_carlo" falsevalue="" checked="false" label="monte_carlo"
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32 help="Perform Monte Carlo analysis on distances. [Default: False]"/>
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33 <param name="suppress_html_output" type="boolean" truevalue="--suppress_html_output" falsevalue="" checked="false" label="suppress_html_output"
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34 help="Suppress HTML format output. [Default: False]"/>
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35 <param name="fields" type="text" label="fields"
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36 help="Comma delimited list of fields to compare. Put list of fields in quotes. This overwrites fields in prefs file. If this is not provided, the first field in metadata mapping file will be used. Usage: --fields 'Field1,Field2,Field3'"/>
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37 <param name="monte_carlo_iters" type="integer" value="100" label="monte_carlo_iters"
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38 help="Number of iterations to perform for Monte Carlo analysis. [default: 100]"/>
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39 </inputs>
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40 <outputs>
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41
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42 </outputs>
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43 <tests>
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44 </tests>
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45 <help>
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46
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47 </help>
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48 </tool>
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