comparison alpha_rarefaction.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
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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