--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jackknifed_beta_diversity.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,101 @@
+<tool id="jackknifed_beta_diversity" name="jackknifed_beta_diversity" version="1.2.1">
+ <description>A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D PCoA plots.</description>
+ <requirements>
+  <requirement type="binary">jackknifed_beta_diversity.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_tmpdir='$__new_file_path__'
+  jackknifed_beta_diversity.py
+  --otu_table_fp=$otu_table_fp
+  --output_dir=$__new_file_path__
+  $force
+  #if $parameter.source == 'hist':
+   --parameter_fp=$parameter_fp
+  #else:
+   --parameter_fp=$parameter_generated
+  #end if
+  --seqs_per_sample=$seqs_per_sample
+  --mapping_fp=$mapping_fp
+  --tree_fp=$tree_fp
+  --master_tree=$master_tree
+  $print_only
+  $parallel
+ </command>
+ <inputs>
+  <param name="otu_table_fp" type="data" format="fasta" label="otu_table_fp"
+   help="the input fasta file [REQUIRED]"/>
+
+  <param name="seqs_per_sample" type="integer" value="-1" label="seqs_per_sample"
+   help="number of sequences to include in each jackknifed subset [REQUIRED]"/>
+  <param name="mapping_fp" type="data" format="tabular" 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">
+   <!--
+        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="txt" label="tree_fp"
+   help="path to the tree file [default: ('NO', 'DEFAULT'); REQUIRED for phylogenetic measures]"/>
+  <param name="master_tree" type="text" value="consensus" label="master_tree"
+   help="method for computing master trees in jackknife analysis. 'consensus': consensus of trees from jackknifed otu tables.  'full': tree generated from input (unsubsambled) otu table.  [default: consensus]"/>
+  <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force"
+   help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/>
+  <param name="print_only" type="boolean" truevalue="--print_only" falsevalue="" checked="false" label="print_only"
+   help="Print the commands but don't call them -- useful for debugging [default: False]"/>
+  <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">
+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>
+ </configfiles>
+
+ <outputs>
+  
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+