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