diff TICCalculator.xml @ 1:1373f6071423 draft

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

--- a/TICCalculator.xml	Wed Mar 01 12:51:22 2017 -0500
+++ b/TICCalculator.xml	Wed Aug 09 09:48:23 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="TICCalculator" name="TICCalculator" version="2.1.0">
+<tool id="TICCalculator" name="TICCalculator" version="2.2.0.1">
   <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
   <macros>
     <token name="@EXECUTABLE@">TICCalculator</token>
@@ -16,10 +16,20 @@
   -in $param_in
 #end if
 #if $param_read_method:
-  -read_method $param_read_method
+  -read_method
+  #if " " in str($param_read_method):
+    "$param_read_method"
+  #else
+    $param_read_method
+  #end if
 #end if
 #if $param_loadData:
-  -loadData $param_loadData
+  -loadData
+  #if " " in str($param_loadData):
+    "$param_loadData"
+  #else
+    $param_loadData
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -29,7 +39,7 @@
 &gt; $param_stdout
 </command>
   <inputs>
-    <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/>
+    <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
     <param name="param_read_method" type="select" optional="False" value="regular" label="Method to read the file" help="(-read_method) ">
       <option value="regular" selected="true">regular</option>
       <option value="indexed">indexed</option>
@@ -47,10 +57,10 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_stdout" format="text" label="Output from stdout"/>
+    <data name="param_stdout" format="txt" label="Output from stdout"/>
   </outputs>
   <help>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/UTILS_TICCalculator.html</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_TICCalculator.html</help>
 </tool>