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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="plot_taxa_summary" name="plot_taxa_summary" version="1.2.1">
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2 <description>Make taxaonomy summary charts based on taxonomy assignment</description>
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3 <requirements>
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4 <requirement type="binary">plot_taxa_summary.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='$__new_file_path__'
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9 plot_taxa_summary.py
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10 --input_files=$input_files
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11 --labels=$labels
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12 --num=$num
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13 --dir-prefix=$dir_prefix
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14 --colorby=$colorby
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15 --prefs_path=$prefs_path
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16 --background_color=$background_color
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17 --dpi=$dpi
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18 --x_width=$x_width
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19 --y_height=$y_height
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20 --bar_width=$bar_width
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21 --type_of_file=$type_of_file
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22 --chart_type=$chart_type
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23 --resize_nth_label=$resize_nth_label
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24 </command>
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25 <inputs>
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26 <param name="input_files" type="data" format="qiimetaxsummary" label="input_files"
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27 help="list of files with sample counts by taxonomy [REQUIRED]"/>
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28 <param name="labels" type="text" label="labels"
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29 help="list of labels (i.e. Phylum, Class) [REQUIRED]"/>
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30 <param name="num" type="text" value="20" label="num"
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31 help="Maximum number of individual categories in each pie chart. All additional categories are grouped into an 'other' category. NOTE: this is only used for the pie charts. [default: 20]"/>
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32 <param name="dir_prefix" type="text" label="dir-prefix"
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33 help="output folder"/>
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34 <param name="colorby" type="text" label="colorby"
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35 help="This is the samples to make 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. [default: %default]"/>
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36 <param name="prefs_path" type="text" label="prefs_path"
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37 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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38 <param name="background_color" type="text" label="background_color"
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39 help="This is the background color to use in the plots. [default: ('NO', 'DEFAULT')]"/>
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40 <param name="dpi" type="text" value="80" label="dpi"
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41 help="This is the dpi to use in the plots. [default: 80]"/>
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42 <param name="x_width" type="text" value="12" label="x_width"
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43 help="This is the width to use in the plots. [default: 12]"/>
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44 <param name="y_height" type="text" value="6" label="y_height"
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45 help="This is the height to use in the plots. [default: 6]"/>
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46 <param name="bar_width" type="text" value="0.75" label="bar_width"
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47 help="This the width of the bars in the bar graph and should be a number between 0 and 1. NOTE: this is only used for bar charts. [default: 0.75]"/>
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48 <param name="type_of_file" type="select" label="type_of_file"
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49 help="This is the filename suffix to use for each high-res plot. (i.e. pdf,svg,png) [default: pdf]">
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50 <option value="pdf" selected="true">pdf</option>
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51 <option value="svg">svg</option>
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52 <option value="png">png</option>
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53 </param>
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54 <param name="chart_type" type="text" value="area,bar" label="chart_type"
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55 help="type of chart to plot (i.e. pie, bar or area). The user has the ability to plot multiple types, by using a comma-separated list (e.g. area,pie) [default: area,bar]"/>
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56 <param name="resize_nth_label" type="text" value="0" label="resize_nth_label"
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57 help="this is for large area and bar charts where the font on the x-axis is small. This allows you to set every nth label to be larger on the x-axis.This requires an integer value greater than 0.[default: 0]"/>
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58 </inputs>
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59 <outputs>
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60 <data name="taxonomy_area_summary_chart" format="html" label="${tool.name} on ${on_string}: taxonomy_area_summary_chart"/>
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61 <data name="taxonomy_bar_summary_chart" format="html" label="${tool.name} on ${on_string}: taxonomy_bar_summary_chart"/>
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62 </outputs>
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63 <tests>
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64 </tests>
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65 <help>
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66
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67 </help>
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68 </tool>
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