Mercurial > repos > jjohnson > qiime
comparison make_prefs_file.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_prefs_file" name="make_prefs_file" version="1.2.1"> | |
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 --galaxy_tmpdir='$__new_file_path__' | |
9 make_prefs_file.py | |
10 --map_fname=$map_fname | |
11 --output_fp=$output_fp | |
12 --mapping_headers_to_use=$mapping_headers_to_use | |
13 --background_color=$background_color | |
14 --monte_carlo_dists=$monte_carlo_dists | |
15 --input_taxa_file=$input_taxa_file | |
16 --ball_scale=$ball_scale | |
17 --arrow_line_color=$arrow_line_color | |
18 --arrow_head_color=$arrow_head_color | |
19 </command> | |
20 <inputs> | |
21 <param name="map_fname" type="data" format="tabular" label="map_fname" | |
22 help="This is the metadata mapping file [default=('NO', 'DEFAULT')] [REQUIRED]"/> | |
23 <param name="mapping_headers_to_use" type="data" format="tabular" label="mapping_headers_to_use" | |
24 help="mapping fields touse in prefs file [default: ALL]"/> | |
25 <param name="background_color" type="text" value="black" label="background_color" | |
26 help="This is the backgroundcolor to use in the plots. [default: black]"/> | |
27 <param name="monte_carlo_dists" type="text" value="10" label="monte_carlo_dists" | |
28 help="monte carlo distanceto use for each sample header [default: 10]"/> | |
29 <param name="input_taxa_file" type="data" format="txt" label="input_taxa_file" | |
30 help="summarized taxa file with samplecounts by taxonomy (resulting file from summarize_taxa.py)"/> | |
31 <param name="ball_scale" type="float" value="1.0" label="ball_scale" | |
32 help="scale factor for the size of each ball in the plots [default: 1.0]"/> | |
33 <param name="arrow_line_color" type="text" value="white" label="arrow_line_color" | |
34 help="arrow line color forprocrustes analysis. [default: white]"/> | |
35 <param name="arrow_head_color" type="text" value="red" label="arrow_head_color" | |
36 help="arrow head color forprocrustes analysis. [default: red]"/> | |
37 </inputs> | |
38 <outputs> | |
39 <data format="txt" name="output_fp"/> | |
40 </outputs> | |
41 <tests> | |
42 </tests> | |
43 <help> | |
44 | |
45 </help> | |
46 </tool> | |
47 |