diff ExternalCalibration.xml @ 0:b9ecf8eba490 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ExternalCalibration.xml	Wed Mar 01 12:46:18 2017 -0500
@@ -0,0 +1,73 @@
+<?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="ExternalCalibration" name="ExternalCalibration" version="2.1.0">
+  <description>Applies an external mass recalibration.</description>
+  <macros>
+    <token name="@EXECUTABLE@">ExternalCalibration</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>ExternalCalibration
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_offset:
+  -offset $param_offset
+#end if
+#if $param_slope:
+  -slope $param_slope
+#end if
+#if $param_power:
+  -power $param_power
+#end if
+
+#if $rep_param_ms_level:
+-ms_level
+  #for token in $rep_param_ms_level:
+    #if " " in str(token):
+      "$token.param_ms_level"
+    #else
+      $token.param_ms_level
+    #end if
+  #end for
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="Input peak file" help="(-in) "/>
+    <param name="param_offset" type="float" value="0.0" label="Mass offset in ppm" help="(-offset) "/>
+    <param name="param_slope" type="float" value="0.0" label="Slope (dependent on m/z)" help="(-slope) "/>
+    <param name="param_power" type="float" value="0.0" label="Power (dependent on m/z)" help="(-power) "/>
+    <repeat name="rep_param_ms_level" min="0" max="1" title="param_ms_level">
+      <param name="param_ms_level" type="text" size="30" value="1 2 3" label="Target MS levels to apply the transformation onto" help="(-ms_level) Scans with other levels remain unchanged">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <expand macro="advanced_options">
+      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" format="mzml"/>
+  </outputs>
+  <help>Applies an external mass recalibration.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ExternalCalibration.html</help>
+</tool>