view beta_diversity.xml @ 0:e5c3175506b7 default tip

Initial tool configs for qiime, most need work.

<tool id="beta_diversity" name="beta_diversity" version="1.2.0">
 <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_tmpdir='$__new_file_path__'
  #set datasets = []
  #if $binary_chisq.__str__ != "None":
   #set  datasets = $datasets + ["'binary_chisq_.*$:'" + $binary_chisq.__str__]
  #end if
  #if $binary_chord.__str__ != "None":
   #set  datasets = $datasets + ["'binary_chord_.*$:'" + $binary_chord.__str__]
  #end if
  #if $binary_euclidean.__str__ != "None":
   #set  datasets = $datasets + ["'binary_euclidean_.*$:'" + $binary_euclidean.__str__]
  #end if
  #if $binary_hamming.__str__ != "None":
   #set  datasets = $datasets + ["'binary_hamming_.*$:'" + $binary_hamming.__str__]
  #end if
  #if $binary_jaccard.__str__ != "None":
   #set  datasets = $datasets + ["'binary_jaccard_.*$:'" + $binary_jaccard.__str__]
  #end if
  #if $binary_lennon.__str__ != "None":
   #set  datasets = $datasets + ["'binary_lennon_.*$:'" + $binary_lennon.__str__]
  #end if
  #if $binary_ochiai.__str__ != "None":
   #set  datasets = $datasets + ["'binary_ochiai_.*$:'" + $binary_ochiai.__str__]
  #end if
  #if $binary_pearson.__str__ != "None":
   #set  datasets = $datasets + ["'binary_pearson_.*$:'" + $binary_pearson.__str__]
  #end if
  #if $binary_sorensen_dice.__str__ != "None":
   #set  datasets = $datasets + ["'binary_sorensen_dice_.*$:'" + $binary_sorensen_dice.__str__]
  #end if
  #if $bray_curtis.__str__ != "None":
   #set  datasets = $datasets + ["'bray_curtis_.*$:'" + $bray_curtis.__str__]
  #end if
  #if $canberra.__str__ != "None":
   #set  datasets = $datasets + ["'canberra_.*$:'" + $canberra.__str__]
  #end if
  #if $chisq.__str__ != "None":
   #set  datasets = $datasets + ["'chisq_.*$:'" + $chisq.__str__]
  #end if
  #if $chord.__str__ != "None":
   #set  datasets = $datasets + ["'chord_.*$:'" + $chord.__str__]
  #end if
  #if $euclidean.__str__ != "None":
   #set  datasets = $datasets + ["'euclidean_.*$:'" + $euclidean.__str__]
  #end if
  #if $gower.__str__ != "None":
   #set  datasets = $datasets + ["'gower_.*$:'" + $gower.__str__]
  #end if
  #if $hellinger.__str__ != "None":
   #set  datasets = $datasets + ["'hellinger_.*$:'" + $hellinger.__str__]
  #end if
  #if $kulczynski.__str__ != "None":
   #set  datasets = $datasets + ["'kulczynski_.*$:'" + $kulczynski.__str__]
  #end if
  #if $manhattan.__str__ != "None":
   #set  datasets = $datasets + ["'manhattan_.*$:'" + $manhattan.__str__]
  #end if
  #if $morisita_horn.__str__ != "None":
   #set  datasets = $datasets + ["'morisita_horn_.*$:'" + $morisita_horn.__str__]
  #end if
  #if $pearson.__str__ != "None":
   #set  datasets = $datasets + ["'pearson_.*$:'" + $pearson.__str__]
  #end if
  #if $soergel.__str__ != "None":
   #set  datasets = $datasets + ["'soergel_.*$:'" + $soergel.__str__]
  #end if
  #if $spearman_approx.__str__ != "None":
   #set  datasets = $datasets + ["'spearman_approx_.*$:'" + $spearman_approx.__str__]
  #end if
  #if $specprof.__str__ != "None":
   #set  datasets = $datasets + ["'specprof_.*$:'" + $specprof.__str__]
  #end if
  #if $unifrac.__str__ != "None":
   #set  datasets = $datasets + ["'unifrac_.*$:'" + $unifrac.__str__]
  #end if
  #if $unifrac_g.__str__ != "None":
   #set  datasets = $datasets + ["'unifrac_g_.*$:'" + $unifrac_g.__str__]
  #end if
  #if $unifrac_g_full_tree.__str__ != "None":
   #set  datasets = $datasets + ["'unifrac_g_full_tree_.*$:'" + $unifrac_g_full_tree.__str__]
  #end if
  #if $unweighted_unifrac.__str__ != "None":
   #set  datasets = $datasets + ["'unweighted_unifrac_.*$:'" + $unweighted_unifrac.__str__]
  #end if
  #if $unweighted_unifrac_full_tree.__str__ != "None":
   #set  datasets = $datasets + ["'unweighted_unifrac_full_tree_.*$:'" + $unweighted_unifrac_full_tree.__str__]
  #end if
  #if $weighted_normalized_unifrac.__str__ != "None":
   #set  datasets = $datasets + ["'weighted_normalized_unifrac_.*$:'" + $weighted_normalized_unifrac.__str__]
  #end if
  #if $weighted_unifrac.__str__ != "None":
   #set  datasets = $datasets + ["'weighted_unifrac_.*$:'" + $weighted_unifrac.__str__]
  #end if
  --galaxy_datasets=#echo ','.join($datasets)
  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"/>
  <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="text"  label="tree_path"
   help="path to newick tree file, required for phylogenetic metrics [default: %default]"/>
  <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>
  
 </help>
</tool>