diff jackknifed_beta_diversity.xml @ 5:205f4c9739c0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380

--- a/jackknifed_beta_diversity.xml	Mon Jul 10 16:42:06 2017 -0400
+++ b/jackknifed_beta_diversity.xml	Sat Aug 05 07:23:59 2017 -0400
@@ -1,5 +1,5 @@
 <tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0">
-    <description>and building jackknifed PCoA plots</description>
+    <description> and building jackknifed PCoA plots (jackknifed_beta_diversity)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -10,25 +10,25 @@
     </stdio>
     <version_command>jackknifed_beta_diversity.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        jackknifed_beta_diversity.py
-            --otu_table_fp '$otu_table_fp'
-            --mapping_fp '$mapping_fp'
-            -o jackknifed_beta_diversity
-            --seqs_per_sample '$seqs_per_sample'
-            #if $tree_fp
-                --tree_fp '$tree_fp'
-            #end if
-            #if $parameter_fp
-                --parameter_fp '$parameter_fp'
-            #end if
-            --master_tree '$master_tree'
-            $parallel
-            -O "\${GALAXY_SLOTS:-4}"
+jackknifed_beta_diversity.py
+    --otu_table_fp '$otu_table_fp'
+    --mapping_fp '$mapping_fp'
+    -o jackknifed_beta_diversity
+    --seqs_per_sample '$seqs_per_sample'
+    #if $tree_fp
+        --tree_fp '$tree_fp'
+    #end if
+    #if $parameter_fp
+        --parameter_fp '$parameter_fp'
+    #end if
+    --master_tree '$master_tree'
+    $parallel
+    -O "\${GALAXY_SLOTS:-4}"
 
-        && python $__tool_directory__/jackknifed_beta_diversity_output_management.py
-            --data_directory jackknifed_beta_diversity
-            --html_file '$jackknifed_beta_diversity_report'
-            --html_dir '$jackknifed_beta_diversity_report.files_path'
+&& python $__tool_directory__/jackknifed_beta_diversity_output_management.py
+    --data_directory jackknifed_beta_diversity
+    --html_file '$jackknifed_beta_diversity_report'
+    --html_dir '$jackknifed_beta_diversity_report.files_path'
     ]]></command>
     <inputs>
         <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/>
@@ -40,7 +40,7 @@
             <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option>
             <option value="full">Tree generated from input (unsubsambled) otu table</option>
         </param>
-        <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/>
+        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
     </inputs>
     <outputs>
         <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity">