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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_otu_network" name="make_otu_network" version="1.2.0">
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2 <description>Make an OTU network and calculate statistics</description>
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3 <requirements>
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4 <requirement type="binary">make_otu_network.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='$__new_file_path__'
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9 make_otu_network.py
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10 --mapping_file=$mapping_file
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11 --input_file=$input_file
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12 --colorby=$colorby
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13 --prefs_path=$prefs_path
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14 --background_color=$background_color
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15 --output_dir=$__new_file_path__
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16 </command>
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17 <inputs>
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18 <param name="mapping_file" type="data" format="tabular" label="mapping_file"
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19 help="name of input map file [REQUIRED]"/>
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20 <param name="input_file" type="data" format="txt" label="input_file"
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21 help="name of otu table file [REQUIRED]"/>
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22 <param name="colorby" type="text" label="colorby"
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23 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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24 <param name="prefs_path" type="text" label="prefs_path"
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25 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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26 <param name="background_color" type="text" label="background_color"
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27 help="This is the background color to use in the plots. [default: ('NO', 'DEFAULT')]"/>
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28 </inputs>
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29 <outputs>
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30
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31 </outputs>
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32 <tests>
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33 </tests>
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34 <help>
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35
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36 </help>
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37 </tool>
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