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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="compare_3d_plots" name="compare_3d_plots" version="1.2.0">
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2 <description>Plot several PCoA files on the same 3D plot</description>
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3 <requirements>
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4 <requirement type="binary">compare_3d_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='$__new_file_path__'
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9 compare_3d_plots.py
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10 --coord_fnames=$coord_fnames
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11 --map_fname=$map_fname
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12 --colorby=$colorby
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13 --custom_axes=$custom_axes
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14 --prefs_path=$prefs_path
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15 --background_color=$background_color
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16 --edges_file=$edges_file
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17 $serial
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18 --output_dir=$__new_file_path__
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19 </command>
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20 <inputs>
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21 <param name="coord_fnames" type="text" label="coord_fnames"
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22 help="This is comma-separated list of the paths to the principal coordinates files (i.e., resulting file from principal_coordinates.py), e.g 'pcoa1.txt,pcoa2.txt' [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 user-generated 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 a list of 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="custom_axes" type="text" label="custom_axes"
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28 help="This is a category or list of categories from the user-generated mapping file to use as a custom axis in the plot. For instance, if there is a pH category and one would like to see the samples plotted on that axis instead of PC1, PC2, etc., one can use this option. It is also useful for plotting time-series data [default: ('NO', 'DEFAULT')]"/>
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29 <param name="prefs_path" type="text" label="prefs_path"
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30 help="This is the user-generated preferences file. NOTE: This is a file with a dictionary containing preferences for the analysis. See make_prefs_file.py. [default: ('NO', 'DEFAULT')]"/>
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31 <param name="background_color" type="text" label="background_color"
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32 help="This is the background color to use in the plots (Options are 'black' or 'white'. [default: ('NO', 'DEFAULT')]"/>
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33 <param name="edges_file" type="data" format="txt" label="edges_file"
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34 help="A file where each line contains two sample IDs separated by a whitespace character; for each pair of sample IDs, an edge will be drawn from the first sample to the second sample. [default: %default]"/>
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35 <param name="serial" type="boolean" truevalue="--serial" falsevalue="" checked="false" label="serial"
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36 help="Connect the 1st set of points to the 2nd, the 2nd to the 3rd, etc. Default behavior is to connect each set of points back to the 1st set. This flag is ignored if the user specifies an edges file."/>
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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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