diff beta_diversity_through_plots.xml @ 5:2140c12755d0 draft

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

--- a/beta_diversity_through_plots.xml	Mon Jul 10 16:43:51 2017 -0400
+++ b/beta_diversity_through_plots.xml	Sat Aug 05 07:17:55 2017 -0400
@@ -1,5 +1,5 @@
-<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices" version="@WRAPPER_VERSION@.0">
-    <description>and generate PCoA plots</description>
+<tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices and generate PCoA plots" version="@WRAPPER_VERSION@.0">
+    <description>(beta_diversity_through_plots)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -9,38 +9,38 @@
     </stdio>
     <version_command>beta_diversity_through_plots.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        beta_diversity_through_plots.py
-            --otu_table_fp '$otu_table_fp'
-            --mapping_fp '$mapping_fp'
-            --output_dir beta_diversity_through_plots
-            #if $tree_fp
-                --tree_fp '$tree_fp'
-            #end if
-            #if $parameter_fp
-                --parameter_fp '$parameter_fp'
-            #end if
-            $color_by_all_fields
-            $parallel
-            -O "\${GALAXY_SLOTS:-4}"
-            #if $seqs_per_sample
-                --seqs_per_sample '$seqs_per_sample'
-            #end if
-            $suppress_emperor_plots
+beta_diversity_through_plots.py
+    --otu_table_fp '$otu_table_fp'
+    --mapping_fp '$mapping_fp'
+    --output_dir beta_diversity_through_plots
+    #if $tree_fp
+        --tree_fp '$tree_fp'
+    #end if
+    #if $parameter_fp
+        --parameter_fp '$parameter_fp'
+    #end if
+    $color_by_all_fields
+    $parallel
+    -O "\${GALAXY_SLOTS:-4}"
+    #if $seqs_per_sample
+        --seqs_per_sample '$seqs_per_sample'
+    #end if
+    $suppress_emperor_plots
 
-        && python $__tool_directory__/beta_diversity_through_plots_html_generation.py
-            --data_directory beta_diversity_through_plots
-            --html_file '$beta_diversity_pcoa'
-            --html_dir '$beta_diversity_pcoa.files_path'
+&& python $__tool_directory__/beta_diversity_through_plots_html_generation.py
+    --data_directory beta_diversity_through_plots
+    --html_file '$beta_diversity_pcoa'
+    --html_dir '$beta_diversity_pcoa.files_path'
     ]]></command>
     <inputs>
-        <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="True" label="OTU table"/>
-        <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="True" label="Mapping file" help=""/>
-        <param argument="--tree_fp" type="data" format="txt" optional="True" label="Tree file (Optional)" help=""/>
+        <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="true" label="OTU table"/>
+        <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="true" label="Mapping file"/>
+        <param argument="--tree_fp" type="data" format="txt" optional="true" label="Tree file (Optional)"/>
         <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
-        <param argument="--color_by_all_fields" type="text" optional="True" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/>
-        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?" help=""/>
-        <param argument="--seqs_per_sample" type="integer" optional="True" label="Depth of coverage for even sampling (Optional)" help=""/>
-        <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="True" label="Generate emperor plots?" help=""/>
+        <param argument="--color_by_all_fields" type="text" optional="true" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/>
+        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="Run in parallel where available?"/>
+        <param argument="--seqs_per_sample" type="integer" optional="true" label="Depth of coverage for even sampling (Optional)"/>
+        <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="true" label="Generate emperor plots?" help=""/>
     </inputs>
     <outputs>
         <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics">