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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_2d_plots" name="make_2d_plots" version="1.2.0">
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2 <description>Make 2D PCoA Plots</description>
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3 <requirements>
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4 <requirement type="binary">make_2d_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='$__new_file_path__'
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9 make_2d_plots.py
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10 --coord_fname=$coord_fname
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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 --ellipsoid_opacity=$ellipsoid_opacity
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16 --ellipsoid_method=$ellipsoid_method
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17 --master_pcoa=$master_pcoa
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18 --output_dir=$__new_file_path__
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19 </command>
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20 <inputs>
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21 <param name="coord_fname" type="text" label="coord_fname"
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22 help="This is the path to the principal coordinates file (i.e., resulting file from principal_coordinates.py). Alternatively, the user can supply a directory containing multiple principal coordinates files. [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="colorby" type="text" label="colorby"
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26 help="This is the categories to color by in the plots from the user-generated mapping file. The categories must match the name of a column header in the mapping file exactly and multiple categories can be list by comma separating them without spaces. The user can also combine columns in the mapping file by separating the categories by '&#38;&#38;' without spaces [default=('NO', 'DEFAULT')]"/>
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27 <param name="prefs_path" type="text" label="prefs_path"
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28 help="This is the user-generated preferences file. NOTE: This is a file with a dictionary containing preferences for the analysis [default: ('NO', 'DEFAULT')]"/>
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29 <param name="background_color" type="text" label="background_color"
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30 help="This is the background color to use in the plots. [default: ('NO', 'DEFAULT')]"/>
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31 <param name="ellipsoid_opacity" type="float" value="0.33" label="ellipsoid_opacity"
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32 help="Used when plotting ellipsoids for a summary plot (i.e. using a directory of coord files instead of a single coordfile). Valid range is 0-1. A value of 0 produces completely transparent (invisible) ellipsoids. A value of 1 produces completely opaque ellipsoids."/>
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33 <param name="ellipsoid_method" type="text" value="IQR" label="ellipsoid_method"
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34 help="Used when plotting ellipsoids for a summary plot (i.e. using a directory of coord files instead of a single coord file). Valid values are 'IQR' and 'sdev'."/>
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35 <param name="master_pcoa" type="text" label="master_pcoa"
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36 help="If performing averaging on multiple coord files, the other coord files will be aligned to this one through procrustes analysis. This master file will not be included in the averaging. If this master coord file is not provided, one of the other coord files will be chosen arbitrarily as the target alignment. [default: %default]"/>
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37 </inputs>
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38 <outputs>
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39
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40 </outputs>
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41 <tests>
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42 </tests>
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43 <help>
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44
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45 </help>
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46 </tool>
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