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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_pie_charts" name="make_pie_charts" version="1.2.0">
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2 <description>Make pie charts based on taxonomy assignment</description>
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3 <requirements>
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4 <requirement type="binary">make_pie_charts.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='$__new_file_path__'
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9 make_pie_charts.py
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10 --input_files=$input_files
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11 --labels=$labels
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12 $sample_flag
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13 --num=$num
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14 --dir-prefix=$dir_prefix
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15 --colorby=$colorby
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16 --prefs_path=$prefs_path
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17 --background_color=$background_color
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18 </command>
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19 <inputs>
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20 <param name="input_files" type="text" label="input_files"
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21 help="list of files with sample counts by taxonomy [REQUIRED]"/>
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22 <param name="labels" type="text" label="labels"
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23 help="list of labels for pie chart(i.e. Phylum,Class)[REQUIRED]"/>
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24 <param name="sample_flag" type="boolean" truevalue="--sample_flag" falsevalue="" checked="false" label="sample_flag"
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25 help="if -s is passed, pie charts will be created for each sample"/>
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26 <param name="num" type="text" value="20" label="num"
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27 help="Maximum number of individual categories in each pie chart. All additional categories are grouped into an 'other' category. [default: 20]"/>
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28 <param name="dir_prefix" type="text" label="dir-prefix"
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29 help="output folder"/>
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30 <param name="colorby" type="text" label="colorby"
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31 help="This is the samples to make pie charts for in the counts files from summarize_taxa.py. The sample name must match the name of a sample id in the header of the counts file exactly and multiple categories can be list by comma separating them without spaces. If you want to see the pie charts broken up by all samples -s is still funtional. If -s is set and -b is used it will just be broken up by all samples. If neither -s or -b are set the pie charts will be based on all samples put together, one for each level. [default: ('NO', 'DEFAULT')]"/>
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32 <param name="prefs_path" type="text" label="prefs_path"
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33 help="This is the user-generated preferences file. NOTE: This is a file with a dictionary containing preferences for the analysis. The label taxonomy_coloring is used for the coloring, see example prefs file preferences_file. [default: ('NO', 'DEFAULT')]"/>
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34 <param name="background_color" type="text" label="background_color"
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35 help="This is the background color to use in the plots. [default: ('NO', 'DEFAULT')]"/>
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36 </inputs>
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37 <outputs>
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38
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39 </outputs>
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40 <tests>
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41 </tests>
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42 <help>
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43
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44 </help>
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45 </tool>
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