Mercurial > repos > jjohnson > qiime
comparison plot_taxa_summary.xml @ 0:e5c3175506b7 default tip
Initial tool configs for qiime, most need work.
| author | Jim Johnson <jj@umn.edu> |
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| date | Sun, 17 Jul 2011 10:30:11 -0500 |
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| -1:000000000000 | 0:e5c3175506b7 |
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| 1 <tool id="plot_taxa_summary" name="plot_taxa_summary" version="1.2.1"> | |
| 2 <description>Make taxaonomy summary charts based on taxonomy assignment</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">plot_taxa_summary.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 plot_taxa_summary.py | |
| 10 --input_files=$input_files | |
| 11 --labels=$labels | |
| 12 --num=$num | |
| 13 --dir-prefix=$dir_prefix | |
| 14 --colorby=$colorby | |
| 15 --prefs_path=$prefs_path | |
| 16 --background_color=$background_color | |
| 17 --dpi=$dpi | |
| 18 --x_width=$x_width | |
| 19 --y_height=$y_height | |
| 20 --bar_width=$bar_width | |
| 21 --type_of_file=$type_of_file | |
| 22 --chart_type=$chart_type | |
| 23 --resize_nth_label=$resize_nth_label | |
| 24 </command> | |
| 25 <inputs> | |
| 26 <param name="input_files" type="data" format="qiimetaxsummary" label="input_files" | |
| 27 help="list of files with sample counts by taxonomy [REQUIRED]"/> | |
| 28 <param name="labels" type="text" label="labels" | |
| 29 help="list of labels (i.e. Phylum, Class) [REQUIRED]"/> | |
| 30 <param name="num" type="text" value="20" label="num" | |
| 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]"/> | |
| 32 <param name="dir_prefix" type="text" label="dir-prefix" | |
| 33 help="output folder"/> | |
| 34 <param name="colorby" type="text" label="colorby" | |
| 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]"/> | |
| 36 <param name="prefs_path" type="text" label="prefs_path" | |
| 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')]"/> | |
| 38 <param name="background_color" type="text" label="background_color" | |
| 39 help="This is the background color to use in the plots. [default: ('NO', 'DEFAULT')]"/> | |
| 40 <param name="dpi" type="text" value="80" label="dpi" | |
| 41 help="This is the dpi to use in the plots. [default: 80]"/> | |
| 42 <param name="x_width" type="text" value="12" label="x_width" | |
| 43 help="This is the width to use in the plots. [default: 12]"/> | |
| 44 <param name="y_height" type="text" value="6" label="y_height" | |
| 45 help="This is the height to use in the plots. [default: 6]"/> | |
| 46 <param name="bar_width" type="text" value="0.75" label="bar_width" | |
| 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]"/> | |
| 48 <param name="type_of_file" type="select" label="type_of_file" | |
| 49 help="This is the filename suffix to use for each high-res plot. (i.e. pdf,svg,png) [default: pdf]"> | |
| 50 <option value="pdf" selected="true">pdf</option> | |
| 51 <option value="svg">svg</option> | |
| 52 <option value="png">png</option> | |
| 53 </param> | |
| 54 <param name="chart_type" type="text" value="area,bar" label="chart_type" | |
| 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]"/> | |
| 56 <param name="resize_nth_label" type="text" value="0" label="resize_nth_label" | |
| 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]"/> | |
| 58 </inputs> | |
| 59 <outputs> | |
| 60 <data name="taxonomy_area_summary_chart" format="html" label="${tool.name} on ${on_string}: taxonomy_area_summary_chart"/> | |
| 61 <data name="taxonomy_bar_summary_chart" format="html" label="${tool.name} on ${on_string}: taxonomy_bar_summary_chart"/> | |
| 62 </outputs> | |
| 63 <tests> | |
| 64 </tests> | |
| 65 <help> | |
| 66 | |
| 67 </help> | |
| 68 </tool> | |
| 69 |