annotate plot_taxa_summary.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="plot_taxa_summary" name="plot_taxa_summary" version="1.2.1">
 <description>Make taxaonomy summary charts based on taxonomy assignment</description>
 <requirements>
  <requirement type="binary">plot_taxa_summary.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_tmpdir='$__new_file_path__'
  plot_taxa_summary.py
  --input_files=$input_files
  --labels=$labels
  --num=$num
  --dir-prefix=$dir_prefix
  --colorby=$colorby
  --prefs_path=$prefs_path
  --background_color=$background_color
  --dpi=$dpi
  --x_width=$x_width
  --y_height=$y_height
  --bar_width=$bar_width
  --type_of_file=$type_of_file
  --chart_type=$chart_type
  --resize_nth_label=$resize_nth_label
 </command>
 <inputs>
  <param name="input_files" type="data" format="qiimetaxsummary"  label="input_files"
   help="list of files with sample counts by taxonomy [REQUIRED]"/>
  <param name="labels" type="text"  label="labels"
   help="list of labels (i.e. Phylum, Class) [REQUIRED]"/>
  <param name="num" type="text" value="20" label="num"
   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]"/>
  <param name="dir_prefix" type="text"  label="dir-prefix"
   help="output folder"/>
  <param name="colorby" type="text"  label="colorby"
   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]"/>
  <param name="prefs_path" type="text"  label="prefs_path"
   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')]"/>
  <param name="background_color" type="text"  label="background_color"
   help="This is the background color to use in the plots. [default: ('NO', 'DEFAULT')]"/>
  <param name="dpi" type="text" value="80" label="dpi"
   help="This is the dpi to use in the plots. [default: 80]"/>
  <param name="x_width" type="text" value="12" label="x_width"
   help="This is the width to use in the plots. [default: 12]"/>
  <param name="y_height" type="text" value="6" label="y_height"
   help="This is the height to use in the plots. [default: 6]"/>
  <param name="bar_width" type="text" value="0.75" label="bar_width"
   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]"/>
  <param name="type_of_file" type="select" label="type_of_file"
   help="This is the filename suffix to use for each high-res plot. (i.e. pdf,svg,png) [default: pdf]">
    <option value="pdf" selected="true">pdf</option>
    <option value="svg">svg</option>
    <option value="png">png</option>
  </param>
  <param name="chart_type" type="text" value="area,bar" label="chart_type"
   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]"/>
  <param name="resize_nth_label" type="text" value="0" label="resize_nth_label"
   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]"/>
 </inputs>
 <outputs>
  <data name="taxonomy_area_summary_chart" format="html" label="${tool.name} on ${on_string}: taxonomy_area_summary_chart"/>
  <data name="taxonomy_bar_summary_chart" format="html" label="${tool.name} on ${on_string}: taxonomy_bar_summary_chart"/>
 </outputs>
 <tests>
 </tests>
 <help>
  
 </help>
</tool>