Mercurial > repos > galaxyp > openms_masstraceextractor

diff MassTraceExtractor.xml @ 1:cd7f683a669a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:57:00 -0400
parents 2fdd110666cb
children 074f89bd9ec9
line wrap: on
line diff
--- a/MassTraceExtractor.xml	Wed Mar 01 12:57:58 2017 -0500
+++ b/MassTraceExtractor.xml	Wed Aug 09 09:57:00 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: [Signal processing and preprocessing]-->
-<tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.1.0">
+<tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.2.0">
   <description>Detects mass traces in centroided LC-MS data.</description>
   <macros>
     <token name="@EXECUTABLE@">MassTraceExtractor</token>
@@ -39,23 +39,48 @@
   -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
 #end if
 #if $param_algorithm_mtd_reestimate_mt_sd:
-  -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd
+  -algorithm:mtd:reestimate_mt_sd
+  #if " " in str($param_algorithm_mtd_reestimate_mt_sd):
+    "$param_algorithm_mtd_reestimate_mt_sd"
+  #else
+    $param_algorithm_mtd_reestimate_mt_sd
+  #end if
 #end if
 #if $param_algorithm_mtd_quant_method:
-  -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method
+  -algorithm:mtd:quant_method
+  #if " " in str($param_algorithm_mtd_quant_method):
+    "$param_algorithm_mtd_quant_method"
+  #else
+    $param_algorithm_mtd_quant_method
+  #end if
 #end if
 #if $param_algorithm_epd_width_filtering:
-  -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering
+  -algorithm:epd:width_filtering
+  #if " " in str($param_algorithm_epd_width_filtering):
+    "$param_algorithm_epd_width_filtering"
+  #else
+    $param_algorithm_epd_width_filtering
+  #end if
 #end if
 #if $param_algorithm_epd_enabled:
-  -algorithm:epd:enabled $param_algorithm_epd_enabled
+  -algorithm:epd:enabled
+  #if " " in str($param_algorithm_epd_enabled):
+    "$param_algorithm_epd_enabled"
+  #else
+    $param_algorithm_epd_enabled
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
   -force
 #end if
     #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
-  -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion
+  -algorithm:mtd:trace_termination_criterion
+  #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
+    "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
+  #else
+    $adv_opts.param_algorithm_mtd_trace_termination_criterion
+  #end if
 #end if
     #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
   -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers