Mercurial > repos > iuc > qiime_summarize_taxa_through_plots

diff summarize_taxa_through_plots.xml @ 5:62eb36dff24d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:16:33 -0400
parents 72b02cea4123
children 834ef917138f
line wrap: on
line diff
--- a/summarize_taxa_through_plots.xml	Mon Jul 10 16:42:50 2017 -0400
+++ b/summarize_taxa_through_plots.xml	Sat Aug 05 07:16:33 2017 -0400
@@ -1,43 +1,43 @@
-<tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="@WRAPPER_VERSION@.0">
-    <description>summaries and plots</description>
+<tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy summaries and plots" version="@WRAPPER_VERSION@.0">
+    <description>(summarize_taxa_through_plots)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <version_command>summarize_taxa_through_plots.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        ## set matplotlib backend
-        export MPLBACKEND="Agg" &&
-        echo "backend:agg" > matplotlibrc &&
+## set matplotlib backend
+export MPLBACKEND="Agg" &&
+echo "backend:agg" > matplotlibrc &&
 
-        summarize_taxa_through_plots.py
-            --otu_table_fp '$otu_table_fp'
-            --output_dir output
-            #if $parameter_fp
-                --parameter_fp '$parameter_fp'
-            #end if
-            #if $mapping.use_mapping == "yes"
-                --mapping_fp '$mapping.mapping_fp'
-                #if str($mapping.mapping_category) != ''
-                    --mapping_category '$mapping.mapping_category'
-                #end if
-            #end if
-            $sort
-        && mkdir -p '$area_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path'
-        && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report'
+summarize_taxa_through_plots.py
+    --otu_table_fp '$otu_table_fp'
+    --output_dir output
+    #if $parameter_fp
+        --parameter_fp '$parameter_fp'
+    #end if
+    #if $mapping.use_mapping == "yes"
+        --mapping_fp '$mapping.mapping_fp'
+        #if str($mapping.mapping_category) != ''
+            --mapping_category '$mapping.mapping_category'
+        #end if
+    #end if
+    $sort
+&& mkdir -p '$area_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path'
+&& mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report'
 
-        && mkdir -p '$bar_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path'
-        && cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path'
-        && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report'
+&& mkdir -p '$bar_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path'
+&& cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path'
+&& mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report'
     ]]></command>
     <inputs>
         <param argument="--otu_table_fp" type="data" format="biom1,tabular,txt" label="Input OTU table"/>
@@ -48,12 +48,12 @@
             </param>
             <when value="yes">
                 <param argument="--mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping"/>
-                <param argument="--mapping_category" type="text" value="" label="Category to use to summarize OTU table" optional="True"/>
+                <param argument="--mapping_category" type="text" value="" optional="true" label="Category to use to summarize OTU table"/>
             </when>
             <when value="no"/>
         </conditional>
-        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/>
-        <param argument="--sort" type="boolean" label="Sort OTU table?" truevalue="--sort" falsevalue="" checked="False"/>
+        <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends"/>
+        <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="" checked="false" label="Sort OTU table?"/>
     </inputs>
     <outputs>
         <collection name="otu_table" type="list" label="${tool.name} on ${on_string}: OTU tables for the different taxonomic levels">