diff MetaProSIP.xml @ 1:a25d96e0d837 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

--- a/MetaProSIP.xml	Wed Mar 01 12:39:28 2017 -0500
+++ b/MetaProSIP.xml	Wed Aug 09 09:29:30 2017 -0400
@@ -1,7 +1,7 @@
 <?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 CTD2Galaxy.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="MetaProSIP" name="MetaProSIP" version="2.1.0">
+<tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1">
   <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaProSIP</token>
@@ -52,13 +52,23 @@
   -weight_merge_window $param_weight_merge_window
 #end if
 #if $param_plot_extension:
-  -plot_extension $param_plot_extension
+  -plot_extension
+  #if " " in str($param_plot_extension):
+    "$param_plot_extension"
+  #else
+    $param_plot_extension
+  #end if
 #end if
 #if $param_qc_output_directory:
   -qc_output_directory     "$param_qc_output_directory"
 #end if
 #if $param_labeling_element:
-  -labeling_element $param_labeling_element
+  -labeling_element
+  #if " " in str($param_labeling_element):
+    "$param_labeling_element"
+  #else
+    $param_labeling_element
+  #end if
 #end if
 #if $param_use_unassigned_ids:
   -use_unassigned_ids
@@ -104,7 +114,12 @@
   -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
 #end if
     #if $adv_opts.param_collect_method:
-  -collect_method $adv_opts.param_collect_method
+  -collect_method
+  #if " " in str($adv_opts.param_collect_method):
+    "$adv_opts.param_collect_method"
+  #else
+    $adv_opts.param_collect_method
+  #end if
 #end if
     #if $adv_opts.param_lowRIA_correlation_threshold:
   -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
@@ -118,7 +133,7 @@
     <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) "/>
     <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
-    <param name="param_r_executable" type="data" format="text" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
+    <param name="param_r_executable" type="data" format="txt" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
     <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
     <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
     <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
@@ -175,5 +190,5 @@
   <help>Performs proteinSIP on peptide features for elemental flux analysis.
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_MetaProSIP.html</help>
+For more information, visit http://www.openms.de/comp/metaprosip/</help>
 </tool>