Mercurial > repos > iuc > qiime_alpha_diversity

diff alpha_diversity.xml @ 5:ffe438e1fc67 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:26:40 -0400
parents 2ceee245d97c
children 1fa3942bec04
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--- a/alpha_diversity.xml	Mon Jul 10 16:42:35 2017 -0400
+++ b/alpha_diversity.xml	Sat Aug 05 07:26:40 2017 -0400
@@ -1,23 +1,23 @@
 <tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="@WRAPPER_VERSION@.0">
-    <description>on each sample in an otu table</description>
+    <description> on each sample in an otu table, using a variety of alpha diversity metrics (alpha_diversity)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>alpha_diversity.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        #set $chosen_metrics = str( $metrics ).split( "," )
-        alpha_diversity.py
-            --input_path '$input_path'
-            -o alphadiv
-            --metrics '$metrics'
-            #if "PD_whole_tree" in $chosen_metrics:
-                --tree_path '$tree_path'
-            #end if
+#set $chosen_metrics = str( $metrics ).split( "," )
+alpha_diversity.py
+    --input_path '$input_path'
+    -o alphadiv
+    --metrics '$metrics'
+    #if "PD_whole_tree" in $chosen_metrics:
+        --tree_path '$tree_path'
+    #end if
     ]]></command>
     <inputs>
         <param argument="--input_path" type="data" format="tabular,txt,tsv,biom" multiple="True"  label="OTU table"/>
-        <param argument="--metrics" type="select" multiple="True"  display="checkboxes" label="Alpha-diversity metric(s) to use">
+        <param argument="--metrics" type="select" multiple="True" display="checkboxes" label="Alpha-diversity metric(s) to use">
             <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option>
             <option value="berger_parker_d">Berger-Parker dominance</option>
             <option value="brillouin_d">Brillouin index of alpha diversity</option>
@@ -50,7 +50,7 @@
             <option value="strong"> Strong’s dominance index</option>
             <option value="PD_whole_tree">Phylogenetic diversity</option>
         </param>
-        <param argument="--tree_path" type="data" format="nhx" optional="True"  label="Newick tree (optional, except for PD_whole_tree metric)"/>
+        <param argument="--tree_path" type="data" format="nhx" optional="true" label="Newick tree (optional, except for PD_whole_tree metric)"/>
     </inputs>
     <outputs>
         <data name="alpha_diversity" format="tabular" from_work_dir="alphadiv" label="${tool.name} on ${on_string}: Alpha diversity"/>