Mercurial > repos > jjohnson > qiime
comparison alpha_rarefaction.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="alpha_rarefaction" name="alpha_rarefaction" version="1.2.0"> | |
2 <description>A workflow script for performing alpha rarefaction</description> | |
3 <requirements> | |
4 <requirement type="binary">alpha_rarefaction.py</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 qiime_wrapper.py | |
8 --galaxy_summary_html='$output_html' | |
9 --galaxy_outputdir='$output_html.extra_files_path' | |
10 --galaxy_summary_template='$output_template' | |
11 ## --galaxy_datasets='^rarefaction_plots.html$:'$output_html | |
12 alpha_rarefaction.py | |
13 --otu_table_fp=$otu_table_fp | |
14 --mapping_fp=$mapping_fp | |
15 --output_dir=$output_html.extra_files_path | |
16 #if $parameter.source == 'hist': | |
17 --parameter_fp=$parameter_fp | |
18 #else: | |
19 --parameter_fp=$parameter_generated | |
20 #end if | |
21 --num_steps=$num_steps | |
22 $force | |
23 $print_only | |
24 $parallel | |
25 #if $tree_fp != None and $tree_fp.__str__ != 'None': | |
26 --tree_fp=$tree_fp | |
27 #end if | |
28 </command> | |
29 <inputs> | |
30 <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp" | |
31 help="the input otu table [REQUIRED]"/> | |
32 <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp" | |
33 help="path to the mapping file [REQUIRED]"/> | |
34 <conditional name="parameter"> | |
35 <param name="source" type="select" label="Parameters from" help=""> | |
36 <option value="hist">Your History</option> | |
37 <option value="build">Build a Parameter file</option> | |
38 </param> | |
39 <when value="hist"> | |
40 <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp" | |
41 help="path to the parameter file [REQUIRED]"/> | |
42 </when> <!-- hist --> | |
43 <when value="build"> | |
44 <!-- | |
45 params['alpha_diversity']['metrics'].split(',') | |
46 params['multiple_rarefactions'] | |
47 params['parallel']) | |
48 params['alpha_diversity']) | |
49 params['collate_alpha'] | |
50 params['make_rarefaction_plots'] | |
51 multiple_rarefactions.py | |
52 min seqs/sample | |
53 max seqs/sample | |
54 step | |
55 depth sequences per sample to subsample | |
56 num-reps | |
57 lineages_included | |
58 keep_empty_otus | |
59 alpha_diversity.py | |
60 collate_alpha.py | |
61 make_rarefaction_plots.py | |
62 --> | |
63 </when> <!-- build --> | |
64 </conditional> <!-- parameter --> | |
65 <param name="num_steps" type="integer" value="10" label="num_steps" | |
66 help="number of steps (or rarefied OTU table sizes) to make between min and max counts [default: 10]"/> | |
67 <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force" | |
68 help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/> | |
69 <param name="print_only" type="boolean" truevalue="--print_only" falsevalue="" checked="false" label="print_only" | |
70 help="Print the commands but don't call them -- useful for debugging [default: False]"/> | |
71 <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel" | |
72 help="Run in parallel where available [default: False]"/> | |
73 <param name="tree_fp" type="data" format="txt" optional="true" label="tree_fp" | |
74 help="path to the tree file [default: REQUIRED for phylogenetic measures]"/> | |
75 </inputs> | |
76 <configfiles> | |
77 <configfile name="parameter_generated"> | |
78 alpha_diversity:metrics chao1,observed_species,PD_whole_tree | |
79 multiple_rarefactions_even_depth:num-reps 20 | |
80 parallel:jobs_to_start 2 | |
81 parallel:retain_temp_files False | |
82 parallel:seconds_to_sleep 60 | |
83 collate_alpha:example_path | |
84 make_rarefaction_plots:imagetype png | |
85 make_rarefaction_plots:resolution 75 | |
86 make_rarefaction_plots:background_color white | |
87 make_rarefaction_plots:prefs_path | |
88 </configfile> | |
89 <configfile name="output_template"> | |
90 <![CDATA[ | |
91 <html> | |
92 <body> | |
93 <a href="rarefaction_plots.html">rarefaction_plots.html</a> | |
94 </body> | |
95 </html> | |
96 ]]> | |
97 </configfile> | |
98 </configfiles> | |
99 <outputs> | |
100 <data format="html" name="output_html" label="alpha_rarefaction_plots"/> | |
101 </outputs> | |
102 <tests> | |
103 </tests> | |
104 <help> | |
105 | |
106 </help> | |
107 </tool> | |
108 |