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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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<tool id="beta_diversity_through_3d_plots" name="beta_diversity_through_3d_plots" version="1.2.0">
 <description>A workflow script for computing beta diversity distance matrices and the corresponding 3D plots</description>
 <requirements>
  <requirement type="binary">beta_diversity_through_3d_plots.py</requirement>
 </requirements>
 <command interpreter="python">
  qiime_wrapper.py
  --galaxy_outputdir='$log.extra_files_path'
  --galaxy_datasets='^log_\S+\.txt$:'$log,'^prefs\.txt$:'$prefs
  beta_diversity_through_3d_plots.py
  --otu_table_fp=$otu_table_fp
  --mapping_fp=$mapping_fp
  --output_dir='$log.extra_files_path'
  --force
  #if $parameter.source == 'hist':
   --parameter_fp=$parameter_fp
  #else:
   --parameter_fp=$parameter_generated
  #end if
  --tree_fp=$tree_fp
  #if int($seqs_per_sample) > 0:
   --seqs_per_sample=$seqs_per_sample
  #end if
  $parallel
 </command>
 <inputs>
  <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
   help="the input OTU table [REQUIRED]"/>
  <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
   help="path to the mapping file [REQUIRED]"/>

  <conditional name="parameter">
   <param name="source" type="select" label="Parameters from" help="">
    <option value="hist">Your History</option>
    <option value="build">Build a Parameter file</option>
   </param>
   <when value="hist">
    <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
     help="path to the parameter file [REQUIRED]"/>
   </when> <!-- hist -->
   <when value="build">
   <!--
     beta_diversity:metrics
        params['alpha_diversity']['metrics'].split(',')
        params['multiple_rarefactions']
        params['parallel'])
        params['alpha_diversity'])
        params['collate_alpha']
        params['make_rarefaction_plots']
    multiple_rarefactions.py
     min seqs/sample
     max seqs/sample
     step
     depth    sequences per sample to subsample
     num-reps
     lineages_included 
     keep_empty_otus
    alpha_diversity.py
    collate_alpha.py
    make_rarefaction_plots.py
   -->
   </when> <!-- build -->
  </conditional> <!-- parameter -->
  <param name="tree_fp" type="data" format="tre" optional="true" label="tree_fp"
   help="path to the tree file [default: ('NO', 'DEFAULT'); REQUIRED for phylogenetic measures]"/>
  <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
   help="depth of coverage for even sampling [default: ('NO', 'DEFAULT')]"/>
  <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
   help="Run in parallel where available [default: False]"/>
 </inputs>
 <configfiles>
  <configfile name="parameter_generated">
beta_diversity:metrics
alpha_diversity:metrics	chao1,observed_species,PD_whole_tree
multiple_rarefactions_even_depth:num-reps	20
parallel:jobs_to_start	2
parallel:retain_temp_files	False
parallel:seconds_to_sleep	60
collate_alpha:example_path
make_rarefaction_plots:imagetype	png
make_rarefaction_plots:resolution	75
make_rarefaction_plots:background_color	white
make_rarefaction_plots:prefs_path
  </configfile>
  <configfile name="output_template">
<![CDATA[
<html>
<body>
<!-- plots discrete/continuous for each beta_diversiry metric txt_3D.html -->
<a href="rarefaction_plots.html">rarefaction_plots.html</a>
</body>
</html>
]]>
  </configfile>

 </configfiles>
 <outputs>
  <!--
This script results in a distance matrix (from beta_diversity.py), 
a principal coordinates file (from principal_coordinates.py), 
a preferences file (from make_prefs_file.py) 
and folder containing the resulting 3d PCoA plots (as an html from make_3d_plots.py).
   -->
  <data format="txt" name="log" label="${tool.name} on ${on_string}: log"/>
  <data format="qiimedistmat" name="seqs_otu_table" label="${tool.name} on ${on_string}: weighted_unifrac_seqs_otu_table_even146.txt"/>
                 {weighted_unifrac}_{dataset_4477.dat}
  <data format="qiimepca" name="pca" label="${tool.name} on ${on_string}: weighted_unifrac_pc.txt"/>
                 
  <data format="qiimeprefs" name="prefs" label="${tool.name} on ${on_string}: prefs.txt"/>
  <data format="html" name="pc_plots" label="${tool.name} on ${on_string}: PCoA plots"/>
 </outputs>
 <tests>
 </tests>
 <help>
$ 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

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
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
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 
principal_coordinates.py -i wf_bdiv_even146_test//weighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//weighted_unifrac_pc.txt 
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
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
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 
principal_coordinates.py -i wf_bdiv_even146_test//unweighted_unifrac_seqs_otu_table_even146.txt -o wf_bdiv_even146_test//unweighted_unifrac_pc.txt 
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
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

  
 </help>
</tool>