Mercurial > repos > galaxyp > openms_proteinquantifier

diff ProteinQuantifier.xml @ 12:b6b03af4724b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:58:53 -0400
parents 645f138c188f
children b40140a6acbe
line wrap: on
line diff
--- a/ProteinQuantifier.xml	Mon Feb 12 08:51:54 2018 -0500
+++ b/ProteinQuantifier.xml	Wed May 15 05:58:53 2019 -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.-->
+<!--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: [Quantitation]-->
-<tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.2.0">
+<tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.3.0">
   <description>Compute peptide and protein abundances</description>
   <macros>
     <token name="@EXECUTABLE@">ProteinQuantifier</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command>ProteinQuantifier
+  <command detect_errors="aggressive"><![CDATA[ProteinQuantifier
 
 #if $param_in:
   -in $param_in
@@ -24,7 +24,7 @@
 #if $param_peptide_out:
   -peptide_out $param_peptide_out
 #end if
-#if $param_top:
+#if str($param_top):
   -top $param_top
 #end if
 #if $param_average:
@@ -72,7 +72,7 @@
   -force
 #end if
 #end if
-</command>
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="featurexml,consensusxml,idxml" optional="False" label="Input file" help="(-in) "/>
     <param name="param_protein_groups" type="data" format="idxml" optional="True" label="Protein inference results for the identification runs that were used to annotate the input (" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). &lt;br&gt;Information about indistinguishable proteins will be used for protein quantification"/>
@@ -121,5 +121,5 @@
   <help>Compute peptide and protein abundances
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_ProteinQuantifier.html</help>
 </tool>