Mercurial > repos > azuzolo > qiime1_3_0
comparison qiime/make_prefs_file.xml @ 0:003162f90751 draft
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| author | azuzolo |
|---|---|
| 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_prefs_file" name="make_prefs_file" version="2.0.0"> | |
| 2 <description>Generate preferences file</description> | |
| 3 <requirements> | |
| 4 <requirement type="binary">make_prefs_file.py</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 7 qiime_wrapper.py | |
| 8 make_prefs_file.py | |
| 9 --map_fname=$map_fname | |
| 10 --output_fp=$output_fp | |
| 11 #if $mapping_headers_to_use != None and $mapping_headers_to_use.__str__ != '': | |
| 12 --mapping_headers_to_use=$mapping_headers_to_use | |
| 13 #end if | |
| 14 --background_color=$background_color | |
| 15 --monte_carlo_dists=$monte_carlo_dists | |
| 16 #if $input_taxa_file != None and $input_taxa_file.__str__ != '' and $input_taxa_file.__str__ != 'None': | |
| 17 --input_taxa_file=$input_taxa_file | |
| 18 #end if | |
| 19 --ball_scale=$ball_scale | |
| 20 --arrow_line_color=$arrow_line_color | |
| 21 --arrow_head_color=$arrow_head_color | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="map_fname" type="data" format="tabular" label="map_fname" | |
| 25 help="This is the metadata mapping file [REQUIRED]"/> | |
| 26 <param name="mapping_headers_to_use" type="text" label="mapping_headers_to_use" | |
| 27 help="mapping fields to use in prefs file [default: leave empty; ALL]"/> | |
| 28 <param name="background_color" type="text" value="black" label="background_color" | |
| 29 help="This is the background color to use in the plots. [default: black]"/> | |
| 30 <param name="monte_carlo_dists" type="text" value="10" label="monte_carlo_dists" | |
| 31 help="monte carlo distanceto use for each sample header [default: 10]"/> | |
| 32 <param name="input_taxa_file" type="data" format="txt" optional="true" label="input_taxa_file" | |
| 33 help="summarized taxa file with samplecounts by taxonomy (resulting file from summarize_taxa.py)"/> | |
| 34 <param name="ball_scale" type="float" value="1.0" label="ball_scale" | |
| 35 help="scale factor for the size of each ball in the plots [default: 1.0]"/> | |
| 36 <param name="arrow_line_color" type="text" value="white" label="arrow_line_color" | |
| 37 help="arrow line color forprocrustes analysis. [default: white]"/> | |
| 38 <param name="arrow_head_color" type="text" value="red" label="arrow_head_color" | |
| 39 help="arrow head color forprocrustes analysis. [default: red]"/> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data format="txt" name="output_fp"/> | |
| 43 </outputs> | |
| 44 <tests> | |
| 45 </tests> | |
| 46 <help>For more information, see make_prefs_file_ in the Qiime documentation. | |
| 47 | |
| 48 Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA | |
| 49 | |
| 50 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN | |
| 51 | |
| 52 .. _make_prefs_file: http://qiime.org/scripts/make_prefs_file.html</help> | |
| 53 </tool> | |
| 54 |