Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/make_rarefaction_plots.xml @ 0:003162f90751 draft
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| author | azuzolo |
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| date | Wed, 06 Jun 2012 16:40:30 -0400 |
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| -1:000000000000 | 0:003162f90751 |
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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_datasets='^\S+\.html$:'$plot | |
| 9 --galaxy_outputdir=$plot.extra_files_path | |
| 10 make_rarefaction_plots.py | |
| 11 --input_dir=$input_dir.extra_files_path | |
| 12 --map_fname=$map_fname | |
| 13 #if $colorby != None and $colorby.__str__ != 'None' and len($colorby.__str__) > 0: | |
| 14 --colorby=$colorby | |
| 15 #end if | |
| 16 #if $prefs_path != None and $prefs_path.__str__ != 'None': | |
| 17 --prefs_path=$prefs_path | |
| 18 #end if | |
| 19 #if $ymax != None and $ymax.__str__ != '': | |
| 20 --ymax=$ymax | |
| 21 #end if | |
| 22 --background_color=$background_color | |
| 23 --imagetype=$imagetype | |
| 24 --resolution=$resolution | |
| 25 --output_dir=$plot.extra_files_path | |
| 26 </command> | |
| 27 <inputs> | |
| 28 <param name="input_dir" type="data" format="txt" label="input_dir" help="Rarefaction file (I.E. log output from collate_alpha). [REQUIRED]"/> | |
| 29 <param name="map_fname" type="data" format="tabular" label="map_fname" help="Name of mapping file [REQUIRED]"/> | |
| 30 <param name="colorby" type="text" label="colorby" help="Name of columns to make rarefaction graphs of, comma delimited, no spaces. [OPTIONAL]"/> | |
| 31 <param name="prefs_path" type="data" format="txt" optional="true" label="prefs_path" help="Preferences file for coloring of columns. [OPTIONAL]"/> | |
| 32 <param name="background_color" type="select" value="white" label="background_color" help="Background color for graphs. [default: white]"> | |
| 33 <option value="white" selected="true">White</option> | |
| 34 <option value="black">Black</option> | |
| 35 </param> | |
| 36 <param name="imagetype" type="select" label="Image Type" | |
| 37 help="Type of image to produce (i.e. pdf,svg,png). [default: png]"> | |
| 38 <option value="pdf">pdf</option> | |
| 39 <option value="svg">svg</option> | |
| 40 <option value="png" selected="true">png</option> | |
| 41 </param> | |
| 42 <param name="resolution" type="integer" value="75" label="resolution" | |
| 43 help="output image resolution, [default: 75]"/> | |
| 44 <param name="ymax" type="text" label="ymax" | |
| 45 help="this is the ymax value to be used for the plots, so you can compare rarefaction plots between two different analyses [default: none]"/> | |
| 46 </inputs> | |
| 47 <outputs> | |
| 48 <data format="html" name="plot" label="${tool.name} on ${on_string}"/> | |
| 49 </outputs> | |
| 50 <tests> | |
| 51 </tests> | |
| 52 <help>This tool takes the log file output from collate_alpha to create an html file of rarefaction plots wherein you can plot by sample and/or by category. | |
| 53 | |
| 54 For more information, see make_rarefaction_plots_ in the Qiime documentation. | |
| 55 | |
| 56 Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA | |
| 57 | |
| 58 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 59 | |
| 60 .. _make_rarefaction_plots: http://qiime.org/scripts/make_rarefaction_plots.html</help> | |
| 61 </tool> | |
| 62 |