Mercurial > repos > jjohnson > qiime
comparison make_rarefaction_plots.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="make_rarefaction_plots" name="make_rarefaction_plots" version="1.2.0"> | |
| 2 <description>Generate Rarefaction Plots</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">make_rarefaction_plots.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 --galaxy_tmpdir='$__new_file_path__' | |
| 9 make_rarefaction_plots.py | |
| 10 --input_dir=$input_dir | |
| 11 --map_fname=$map_fname | |
| 12 --colorby=$colorby | |
| 13 --prefs_path=$prefs_path | |
| 14 --background_color=$background_color | |
| 15 --imagetype=$imagetype | |
| 16 --resolution=$resolution | |
| 17 --ymax=$ymax | |
| 18 $webpage | |
| 19 --output_dir=$__new_file_path__ | |
| 20 </command> | |
| 21 <inputs> | |
| 22 <param name="input_dir" type="text" label="input_dir" | |
| 23 help="name of folder containing rarefaction files, takes output from collate_alpha.py. The user can also supply a list of files, which are comma-separated. [REQUIRED]"/> | |
| 24 <param name="map_fname" type="data" format="tabular" label="map_fname" | |
| 25 help="name of mapping file [REQUIRED]"/> | |
| 26 <param name="colorby" type="text" label="colorby" | |
| 27 help="name of columns to make rarefaction graphs of, comma delimited no spaces."/> | |
| 28 <param name="prefs_path" type="text" label="prefs_path" | |
| 29 help="preferences file for coloring of columns."/> | |
| 30 <param name="background_color" type="text" value="white" label="background_color" | |
| 31 help="Background color for graphs."/> | |
| 32 <param name="imagetype" type="text" value="png" label="imagetype" | |
| 33 help="extension for image type choose from (png, svg, pdf). WARNING: Some formats may not properly open in your browser! [default: png]"/> | |
| 34 <param name="resolution" type="integer" value="75" label="resolution" | |
| 35 help="output image resolution, [default: 75]"/> | |
| 36 <param name="ymax" type="integer" value="-1" label="ymax" | |
| 37 help="this is the ymax value to be used for the plots, so you can compare rarefaction plots between two different analyses [default: ('NO', 'DEFAULT')]"/> | |
| 38 <param name="webpage" type="boolean" truevalue="" falsevalue="--webpage" checked="false" label="webpage" | |
| 39 help="this is allows to user to not create the webpage, which may be slow with large datasets [default: True]"/> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 | |
| 43 </outputs> | |
| 44 <tests> | |
| 45 </tests> | |
| 46 <help> | |
| 47 | |
| 48 </help> | |
| 49 </tool> | |
| 50 |