--- a/MetaProSIP.xml	Mon Feb 12 12:54:44 2018 -0500
+++ b/MetaProSIP.xml	Tue Mar 20 14:37:53 2018 -0400
@@ -1,18 +1,19 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="MetaProSIP" name="MetaProSIP" version="2.3.0">
+<tool id="MetaProSIP" name="MetaProSIP" version="2.3.1">
   <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaProSIP</token>
     <import>macros.xml</import>
   </macros>
-  <expand macro="references"/>
-  <expand macro="stdio"/>
   <expand macro="requirements">
     <requirement type="package" version="3.4.1">r-base</requirement>
+    <requirement type="package" version="3.0.1">r-gplots</requirement>
   </expand>
-  <command>MetaProSIP
+  <expand macro="stdio"/>
+  <command><![CDATA[
+MetaProSIP
 
 #if $param_in_mzML:
   -in_mzML $param_in_mzML
@@ -58,8 +59,10 @@
     $param_plot_extension
   #end if
 #end if
-#if $param_qc_output_directory:
-  -qc_output_directory     "$param_qc_output_directory"
+#if $param_plot_extension == 'pdf':
+  -qc_output_directory images
+#else
+  -qc_output_directory '${html_file.files_path}'
 #end if
 #if $param_labeling_element:
   -labeling_element
@@ -127,7 +130,16 @@
   -force
 #end if
 #end if
-</command>
+-threads "\${GALAXY_SLOTS:-1}"
+
+## remove urls and paths (keeping the file name basename)
+&& sed -i -e 's/file:\/\/[^[:space:]]\+\///g; s/\/[^[:space:]]\+\///g' $param_out_csv 
+
+## get html file (should be only one [?])
+#if $param_plot_extension != 'pdf':
+  && cp '${html_file.files_path}'/*\.html output.html
+#end if
+ ]]></command>
   <inputs>
     <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
     <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
@@ -144,14 +156,6 @@
       <option value="svg">svg</option>
       <option value="pdf">pdf</option>
     </param>
-    <param name="param_qc_output_directory" type="text" size="30" label="Output directory for the quality report" help="(-qc_output_directory) ">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
     <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
       <option value="C" selected="true">C</option>
       <option value="N">N</option>
@@ -182,11 +186,28 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_out_csv" format="tabular"/>
-    <data name="param_out_peptide_centric_csv" format="tabular"/>
+    <data name="param_out_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/>
+    <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/>
+    <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage">
+      <filter>param_plot_extension == 'png' or param_plot_extension == 'svg'</filter>
+    </data>
+    <collection name="images" type="list" label="${tool.name} on ${on_string}: images">
+      <filter>param_plot_extension == 'pdf'</filter>
+      <discover_datasets pattern="__name_and_ext__" directory="images" />
+    </collection>
   </outputs>
+  <tests>
+    <test>
+      <param name="param_in_mzML" value="MetaProSIP_1_input.mzML"/>
+      <param name="param_in_fasta" value="MetaProSIP_1_input.fasta"/>
+      <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML"/>
+      <output name="param_out_csv" file="MetaProSIP_1_output_1.csv" />
+      <output name="param_out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" />
+    </test>
+  </tests>
   <help>Performs proteinSIP on peptide features for elemental flux analysis.
 
 
 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html</help>
+<expand macro="references"/>
 </tool>