--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime/beta_diversity.xml	Wed Jun 06 16:40:30 2012 -0400
@@ -0,0 +1,351 @@
+<tool id="beta_diversity" name="beta_diversity" version="2.0.0">
+ <description>Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables</description>
+ <requirements>
+  <requirement type="binary">beta_diversity.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_outputdir=$__new_file_path__
+  #set datasets = []
+  #set $path = ""
+  #if $binary_chisq.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_chisq_.*$:'" + $binary_chisq.__str__]
+   #if path == "":
+   #set $path=$binary_chisq.extra_files_path
+   #end if
+  #end if
+  #if $binary_chord.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_chord_.*$:'" + $binary_chord.__str__]
+   #if path == "":
+   #set $path=$binary_chord.extra_files_path
+   #end if
+  #end if
+  #if $binary_euclidean.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_euclidean_.*$:'" + $binary_euclidean.__str__]
+   #if path == "":
+   #set $path=$binary_euclidean.extra_files_path
+   #end if
+  #end if
+  #if $binary_hamming.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_hamming_.*$:'" + $binary_hamming.__str__]
+   #if path == "":
+   #set $path=$binary_hamming.extra_files_path
+   #end if
+  #end if
+  #if $binary_jaccard.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_jaccard_.*$:'" + $binary_jaccard.__str__]
+   #if path == "":
+   #set $path=$binary_jaccard.extra_files_path
+   #end if
+  #end if
+  #if $binary_lennon.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_lennon_.*$:'" + $binary_lennon.__str__]
+   #if path == "":
+   #set $path=$binary_lennon.extra_files_path
+   #end if
+  #end if
+  #if $binary_ochiai.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_ochiai_.*$:'" + $binary_ochiai.__str__]
+   #if path == "":
+   #set $path=$binary_ochiai.extra_files_path
+   #end if
+  #end if
+  #if $binary_pearson.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_pearson_.*$:'" + $binary_pearson.__str__]
+   #if path == "":
+   #set $path=$binary_pearson.extra_files_path
+   #end if
+  #end if
+  #if $binary_sorensen_dice.__str__ != "None":
+   #set  datasets = $datasets + ["'binary_sorensen_dice_.*$:'" + $binary_sorensen_dice.__str__]
+   #if path == "":
+   #set $path=$binary_sorensen.extra_files_path
+   #end if
+  #end if
+  #if $bray_curtis.__str__ != "None":
+   #set  datasets = $datasets + ["'bray_curtis_.*$:'" + $bray_curtis.__str__]
+   #if path == "":
+   #set $path=$bray_curtis.extra_files_path
+   #end if
+  #end if
+  #if $canberra.__str__ != "None":
+   #set  datasets = $datasets + ["'canberra_.*$:'" + $canberra.__str__]
+   #if path == "":
+   #set $path=$canberra.extra_files_path
+   #end if
+  #end if
+  #if $chisq.__str__ != "None":
+   #set  datasets = $datasets + ["'chisq_.*$:'" + $chisq.__str__]
+   #if path == "":
+   #set $path=$binary_euclidean.extra_files_path
+   #end if
+  #end if
+  #if $chord.__str__ != "None":
+   #set  datasets = $datasets + ["'chord_.*$:'" + $chord.__str__]
+   #if path == "":
+   #set $path=$chord.extra_files_path
+   #end if
+  #end if
+  #if $euclidean.__str__ != "None":
+   #set  datasets = $datasets + ["'euclidean_.*$:'" + $euclidean.__str__]
+   #if path == "":
+   #set $path=$euclidean.extra_files_path
+   #end if
+  #end if
+  #if $gower.__str__ != "None":
+   #set  datasets = $datasets + ["'gower_.*$:'" + $gower.__str__]
+   #if path == "":
+   #set $path=$gower.extra_files_path
+   #end if
+  #end if
+  #if $hellinger.__str__ != "None":
+   #set  datasets = $datasets + ["'hellinger_.*$:'" + $hellinger.__str__]
+   #if path == "":
+   #set $path=$hellinger.extra_files_path
+   #end if
+  #end if
+  #if $kulczynski.__str__ != "None":
+   #set  datasets = $datasets + ["'kulczynski_.*$:'" + $kulczynski.__str__]
+   #if path == "":
+   #set $path=$kulczynski.extra_files_path
+   #end if
+  #end if
+  #if $manhattan.__str__ != "None":
+   #set  datasets = $datasets + ["'manhattan_.*$:'" + $manhattan.__str__]
+   #if path == "":
+   #set $path=$manhattan.extra_files_path
+   #end if
+  #end if
+  #if $morisita_horn.__str__ != "None":
+   #set  datasets = $datasets + ["'morisita_horn_.*$:'" + $morisita_horn.__str__]
+   #if path == "":
+   #set $path=$morisita_horn.extra_files_path
+   #end if
+  #end if
+  #if $pearson.__str__ != "None":
+   #set  datasets = $datasets + ["'pearson_.*$:'" + $pearson.__str__]
+   #if path == "":
+   #set $path=$pearson.extra_files_path
+   #end if
+  #end if
+  #if $soergel.__str__ != "None":
+   #set  datasets = $datasets + ["'soergel_.*$:'" + $soergel.__str__]
+   #if path == "":
+   #set $path=$soergel.extra_files_path
+   #end if
+  #end if
+  #if $spearman_approx.__str__ != "None":
+   #set  datasets = $datasets + ["'spearman_approx_.*$:'" + $spearman_approx.__str__]
+   #if path == "":
+   #set $path=$spearman_approx.extra_files_path
+   #end if
+  #end if
+  #if $specprof.__str__ != "None":
+   #set  datasets = $datasets + ["'specprof_.*$:'" + $specprof.__str__]
+   #if path == "":
+   #set $path=$specprof.extra_files_path
+   #end if
+  #end if
+  #if $unifrac.__str__ != "None":
+   #set  datasets = $datasets + ["'unifrac_.*$:'" + $unifrac.__str__]
+   #if path == "":
+   #set $path=$unifrac.extra_files_path
+   #end if
+  #end if
+  #if $unifrac_g.__str__ != "None":
+   #set  datasets = $datasets + ["'unifrac_g_.*$:'" + $unifrac_g.__str__]
+   #if path == "":
+   #set $path=$unifrac_g.extra_files_path
+   #end if
+  #end if
+  #if $unifrac_g_full_tree.__str__ != "None":
+   #set  datasets = $datasets + ["'unifrac_g_full_tree_.*$:'" + $unifrac_g_full_tree.__str__]
+   #if path == "":
+   #set $path=$unifrac_g_full_tree.extra_files_path
+   #end if
+  #end if
+  #if $unweighted_unifrac.__str__ != "None":
+   #set  datasets = $datasets + ["'unweighted_unifrac_.*$:'" + $unweighted_unifrac.__str__]
+   #if path == "":
+   #set $path=$unweighted_unifrac.extra_files_path
+   #end if
+  #end if
+  #if $unweighted_unifrac_full_tree.__str__ != "None":
+   #set  datasets = $datasets + ["'unweighted_unifrac_full_tree_.*$:'" + $unweighted_unifrac_full_tree.__str__]
+   #if path == "":
+   #set $path=$unweighted_unifrac_full_tree.extra_files_path
+   #end if
+  #end if
+  #if $weighted_normalized_unifrac.__str__ != "None":
+   #set  datasets = $datasets + ["'weighted_normalized_unifrac_.*$:'" + $weighted_normalized_unifrac.__str__]
+   #if path == "":
+   #set $path=$weighted_normalized_unifrac.extra_files_path
+   #end if
+  #end if
+  #if $weighted_unifrac.__str__ != "None":
+   #set  datasets = $datasets + ["'weighted_unifrac_.*$:'" + $weighted_unifrac.__str__]
+   #if path == "":
+   #set $path=$weighted_unifrac.extra_files_path
+   #end if
+  #end if
+  --galaxy_datasets=#echo ','.join($datasets)
+  --galaxy_new_files_path='$path'
+  beta_diversity.py
+  --input_path=$input_path
+  #if $rows.__str__ != '':
+   --rows=$rows
+  #end if
+  --output_dir=$__new_file_path__
+  --metrics=$metrics
+  #if $tree_path.__str__ != "None" and len($tree_path.__str__) > 0:
+   --tree_path=$tree_path
+  #end if
+  $full_tree
+ </command>
+ <inputs>
+  <param name="input_path" type="data" format="qiimeotutable"  label="input_path"
+   help="input path: otu table (e.g., output from make_otu_table or single_rarefaction)"/>
+  <param name="rows" type="text"  label="rows"
+   help="compute only these rows of the distance matrix. pass a list of sample names, e.g. 's1,s3' [by default, +      the full n x n matrix is generated]"/>
+  <param name="metrics" type="select" multiple="true"  label="metrics" help="metrics to use">
+    <option value="abund_jaccard">abund_jaccard</option>
+    <option value="binary_chisq">binary_chisq</option>
+    <option value="binary_chord">binary_chord</option>
+    <option value="binary_euclidean">binary_euclidean</option>
+    <option value="binary_hamming">binary_hamming</option>
+    <option value="binary_jaccard">binary_jaccard</option>
+    <option value="binary_lennon">binary_lennon</option>
+    <option value="binary_ochiai">binary_ochiai</option>
+    <option value="binary_otu_gain">binary_otu_gain</option>
+    <option value="binary_pearson">binary_pearson</option>
+    <option value="binary_sorensen_dice">binary_sorensen_dice</option>
+    <option value="bray_curtis">bray_curtis</option>
+    <option value="canberra">canberra</option>
+    <option value="chisq">chisq</option>
+    <option value="chord">chord</option>
+    <option value="euclidean">euclidean</option>
+    <option value="gower">gower</option>
+    <option value="hellinger">hellinger</option>
+    <option value="kulczynski">kulczynski</option>
+    <option value="manhattan">manhattan</option>
+    <option value="morisita_horn">morisita_horn</option>
+    <option value="pearson">pearson</option>
+    <option value="soergel">soergel</option>
+    <option value="spearman_approx">spearman_approx</option>
+    <option value="specprof">specprof</option>
+    <option value="unifrac">unifrac</option>
+    <option value="unifrac_g">unifrac_g</option>
+    <option value="unifrac_g_full_tree">unifrac_g_full_tree</option>
+    <option value="unweighted_unifrac">unweighted_unifrac</option>
+    <option value="unweighted_unifrac_full_tree">unweighted_unifrac_full_tree</option>
+    <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option>
+    <option value="weighted_unifrac">weighted_unifrac</option>
+  </param>
+  <param name="tree_path" type="data" optional="true" label="tree_path"
+   help="path to newick tree file, required for phylogenetic metrics [default: None]"/>
+  <param name="full_tree" type="boolean" truevalue="--full_tree" falsevalue="" checked="false" label="full_tree"
+   help="by default, we first compute the intersection of the tree with the otus present in the otu table. pass -f if you already have a minimal tree, and this script will run faster"/>
+ </inputs>
+ <outputs>
+  <data format="qiimedistmat" name="binary_chisq" label="${tool.name} on ${on_string}: binary_chisq.dist">
+   <filter>'binary_chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_chord" label="${tool.name} on ${on_string}: binary_chord.dist">
+   <filter>'binary_chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_euclidean" label="${tool.name} on ${on_string}: binary_euclidean.dist">
+   <filter>'binary_euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_hamming" label="${tool.name} on ${on_string}: binary_hamming.dist">
+   <filter>'binary_hamming' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_jaccard" label="${tool.name} on ${on_string}: binary_jaccard.dist">
+   <filter>'binary_jaccard' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_lennon" label="${tool.name} on ${on_string}: binary_lennon.dist">
+   <filter>'binary_lennon' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_ochiai" label="${tool.name} on ${on_string}: binary_ochiai.dist">
+   <filter>'binary_ochiai' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_pearson" label="${tool.name} on ${on_string}: binary_pearson.dist">
+   <filter>'binary_pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="binary_sorensen_dice" label="${tool.name} on ${on_string}: binary_sorensen_dice.dist">
+   <filter>'binary_sorensen_dice' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="bray_curtis" label="${tool.name} on ${on_string}: bray_curtis.dist">
+   <filter>'bray_curtis' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="canberra" label="${tool.name} on ${on_string}: canberra.dist">
+   <filter>'canberra' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="chisq" label="${tool.name} on ${on_string}: chisq.dist">
+   <filter>'chisq' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="chord" label="${tool.name} on ${on_string}: chord.dist">
+   <filter>'chord' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="euclidean" label="${tool.name} on ${on_string}: euclidean.dist">
+   <filter>'euclidean' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="gower" label="${tool.name} on ${on_string}: gower.dist">
+   <filter>'gower' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="hellinger" label="${tool.name} on ${on_string}: hellinger.dist">
+   <filter>'hellinger' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="kulczynski" label="${tool.name} on ${on_string}: kulczynski.dist">
+   <filter>'kulczynski' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="manhattan" label="${tool.name} on ${on_string}: manhattan.dist">
+   <filter>'manhattan' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="morisita_horn" label="${tool.name} on ${on_string}: morisita_horn.dist">
+   <filter>'morisita_horn' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="pearson" label="${tool.name} on ${on_string}: pearson.dist">
+   <filter>'pearson' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="soergel" label="${tool.name} on ${on_string}: soergel.dist">
+   <filter>'soergel' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="spearman_approx" label="${tool.name} on ${on_string}: spearman_approx.dist">
+   <filter>'spearman_approx' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="specprof" label="${tool.name} on ${on_string}: specprof.dist">
+   <filter>'specprof' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="unifrac" label="${tool.name} on ${on_string}: unifrac.dist">
+   <filter>'unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="unifrac_g" label="${tool.name} on ${on_string}: unifrac_g.dist">
+   <filter>'unifrac_g' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="unifrac_g_full_tree" label="${tool.name} on ${on_string}: unifrac_g_full_tree.dist">
+   <filter>'unifrac_g_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="unweighted_unifrac" label="${tool.name} on ${on_string}: unweighted_unifrac.dist">
+   <filter>'unweighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="unweighted_unifrac_full_tree" label="${tool.name} on ${on_string}: unweighted_unifrac_full_tree.dist">
+   <filter>'unweighted_unifrac_full_tree' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="weighted_normalized_unifrac" label="${tool.name} on ${on_string}: weighted_normalized_unifrac.dist">
+   <filter>'weighted_normalized_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+  <data format="qiimedistmat" name="weighted_unifrac" label="${tool.name} on ${on_string}: weighted_unifrac.dist">
+   <filter>'weighted_unifrac' in (metrics if isinstance(metrics,list) else [metrics])</filter>
+  </data>
+ </outputs>
+ <tests>
+ </tests>
+ <help>For more information, see beta_diversity_ in the Qiime documentation.
+ 
+Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
+
+Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
+ 
+ .. _beta_diversity: http://qiime.org/scripts/beta_diversity.html</help>
+</tool>
+