diff plot_taxa_summary.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_taxa_summary.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,69 @@
+<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>
+