Mercurial > repos > jjohnson > qiime

comparison beta_diversity_through_3d_plots.xml @ 0:e5c3175506b7 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:e5c3175506b7
1 <tool id="beta_diversity_through_3d_plots" name="beta_diversity_through_3d_plots" version="1.2.0">
2 <description>A workflow script for computing beta diversity distance matrices and the corresponding 3D plots</description>
3 <requirements>
4 <requirement type="binary">beta_diversity_through_3d_plots.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 --galaxy_outputdir='$log.extra_files_path'
9 --galaxy_datasets='^log_\S+\.txt$:'$log,'^prefs\.txt$:'$prefs
10 beta_diversity_through_3d_plots.py
11 --otu_table_fp=$otu_table_fp
12 --mapping_fp=$mapping_fp
13 --output_dir='$log.extra_files_path'
14 --force
15 #if $parameter.source == 'hist':
16 --parameter_fp=$parameter_fp
17 #else:
18 --parameter_fp=$parameter_generated
19 #end if
20 --tree_fp=$tree_fp
21 #if int($seqs_per_sample) > 0:
22 --seqs_per_sample=$seqs_per_sample
23 #end if
24 $parallel
25 </command>
26 <inputs>
27 <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
28 help="the input OTU table [REQUIRED]"/>
29 <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
30 help="path to the mapping file [REQUIRED]"/>
31
32 <conditional name="parameter">
33 <param name="source" type="select" label="Parameters from" help="">
34 <option value="hist">Your History</option>
35 <option value="build">Build a Parameter file</option>
36 </param>
37 <when value="hist">
38 <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
39 help="path to the parameter file [REQUIRED]"/>
40 </when> <!-- hist -->
41 <when value="build">
42 <!--
43 beta_diversity:metrics
44 params['alpha_diversity']['metrics'].split(',')
45 params['multiple_rarefactions']
46 params['parallel'])
47 params['alpha_diversity'])
48 params['collate_alpha']
49 params['make_rarefaction_plots']
50 multiple_rarefactions.py
51 min seqs/sample
52 max seqs/sample
53 step
54 depth sequences per sample to subsample
55 num-reps
56 lineages_included
57 keep_empty_otus
58 alpha_diversity.py
59 collate_alpha.py
60 make_rarefaction_plots.py
61 -->
62 </when> <!-- build -->
63 </conditional> <!-- parameter -->
64 <param name="tree_fp" type="data" format="tre" optional="true" label="tree_fp"
65 help="path to the tree file [default: ('NO', 'DEFAULT'); REQUIRED for phylogenetic measures]"/>
66 <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
67 help="depth of coverage for even sampling [default: ('NO', 'DEFAULT')]"/>
68 <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
69 help="Run in parallel where available [default: False]"/>
70 </inputs>
71 <configfiles>
72 <configfile name="parameter_generated">
73 beta_diversity:metrics
74 alpha_diversity:metrics chao1,observed_species,PD_whole_tree
75 multiple_rarefactions_even_depth:num-reps 20
76 parallel:jobs_to_start 2
77 parallel:retain_temp_files False
78 parallel:seconds_to_sleep 60
79 collate_alpha:example_path
80 make_rarefaction_plots:imagetype png
81 make_rarefaction_plots:resolution 75
82 make_rarefaction_plots:background_color white
83 make_rarefaction_plots:prefs_path
84 </configfile>
85 <configfile name="output_template">
86 <![CDATA[
87 <html>
88 <body>
89 <!-- plots discrete/continuous for each beta_diversiry metric txt_3D.html -->
90 <a href="rarefaction_plots.html">rarefaction_plots.html</a>
91 </body>
92 </html>
93 ]]>
94 </configfile>
95
96 </configfiles>
97 <outputs>
98 <!--
99 This script results in a distance matrix (from beta_diversity.py),
100 a principal coordinates file (from principal_coordinates.py),
101 a preferences file (from make_prefs_file.py)
102 and folder containing the resulting 3d PCoA plots (as an html from make_3d_plots.py).
103 -->
104 <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
105 <data format="qiimedistmat" name="seqs_otu_table" label="${tool.name} on ${on_string}: weighted_unifrac_seqs_otu_table_even146.txt"/>
106 {weighted_unifrac}_{dataset_4477.dat}
107 <data format="qiimepca" name="pca" label="${tool.name} on ${on_string}: weighted_unifrac_pc.txt"/>
108
109 <data format="qiimeprefs" name="prefs" label="${tool.name} on ${on_string}: prefs.txt"/>
110 <data format="html" name="pc_plots" label="${tool.name} on ${on_string}: PCoA plots"/>
111 </outputs>
112 <tests>
113 </tests>
114 <help>
115 $ beta_diversity_through_3d_plots.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -m Fasting_Map.txt -o wf_bdiv_even146_test/ -p custom_parameters.tt -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre -e 146 --print_only
116
117 single_rarefaction.py -i wf_da/uclust_picked_otus/rep_set/rdp_assigned_taxonomy/otu_table/seqs_otu_table.txt -o wf_bdiv_even146_test//seqs_otu_table_even146.txt -d 146
118 make_prefs_file.py -m Fasting_Map.txt -o wf_bdiv_even146_test//prefs.txt --monte_carlo_dists 10 --background_color black --mapping_headers_to_use Treatment,DOB
119 beta_diversity.py -i wf_bdiv_even146_test//seqs_otu_table_even146.txt -o wf_bdiv_even146_test/ --metrics weighted_unifrac -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre
120 principal_coordinates.py -i wf_bdiv_even146_test//weighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//weighted_unifrac_pc.txt
121 make_3d_plots.py -p wf_bdiv_even146_test//prefs.txt -i wf_bdiv_even146_test//weighted_unifrac_pc.txt -o wf_bdiv_even146_test//weighted_unifrac_3d_continuous/ -m Fasting_Map.txt --ellipsoid_smoothness 1
122 make_3d_plots.py -b "SampleID,BarcodeSequence,LinkerPrimerSequence,Treatment,DOB,Description" -i wf_bdiv_even146_test//weighted_unifrac_pc.txt -o wf_bdiv_even146_test//weighted_unifrac_3d_discrete/ -m Fasting_Map.txt --ellipsoid_smoothness 1
123 beta_diversity.py -i wf_bdiv_even146_test//seqs_otu_table_even146.txt -o wf_bdiv_even146_test/ --metrics unweighted_unifrac -t wf_da/uclust_picked_otus/rep_set/pynast_aligned_seqs/fasttree_phylogeny/seqs_rep_set.tre
124 principal_coordinates.py -i wf_bdiv_even146_test//unweighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//unweighted_unifrac_pc.txt
125 make_3d_plots.py -p wf_bdiv_even146_test//prefs.txt -i wf_bdiv_even146_test//unweighted_unifrac_pc.txt -o wf_bdiv_even146_test//unweighted_unifrac_3d_continuous/ -m Fasting_Map.txt --ellipsoid_smoothness 1
126 make_3d_plots.py -b "SampleID,BarcodeSequence,LinkerPrimerSequence,Treatment,DOB,Description" -i wf_bdiv_even146_test//unweighted_unifrac_pc.txt -o wf_bdiv_even146_test//unweighted_unifrac_3d_discrete/ -m Fasting_Map.txt --ellipsoid_smoothness 1
127
128
129 </help>
130 </tool>
131