diff PrecursorMassCorrector.xml @ 0:7788e4d10cc6 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/PrecursorMassCorrector.xml	Wed Mar 01 12:52:00 2017 -0500
@@ -0,0 +1,56 @@
+<?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="PrecursorMassCorrector" name="PrecursorMassCorrector" version="2.1.0">
+  <description>Corrects the precursor entries of MS/MS spectra, by using MS1 information.</description>
+  <macros>
+    <token name="@EXECUTABLE@">PrecursorMassCorrector</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>PrecursorMassCorrector
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_feature_in:
+  -feature_in $param_feature_in
+#end if
+#if $param_precursor_mass_tolerance:
+  -precursor_mass_tolerance $param_precursor_mass_tolerance
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_max_charge:
+  -max_charge $adv_opts.param_max_charge
+#end if
+    #if $adv_opts.param_intensity_threshold:
+  -intensity_threshold $adv_opts.param_intensity_threshold
+#end if
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzml" optional="False" label="Input mzML file containing the spectra" help="(-in) "/>
+    <param name="param_feature_in" type="data" format="featurexml" optional="True" label="Input featureXML file, containing features; if set, the MS/MS spectra precursor entries  &lt;br&gt;will be matched to the feature m/z values if possible" help="(-feature_in) "/>
+    <param name="param_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="1.5" label="Maximal deviation in Th which is acceptable to be corrected; &lt;br&gt;this value should be set to the instruments selection window" help="(-precursor_mass_tolerance) "/>
+    <expand macro="advanced_options">
+      <param name="param_max_charge" type="integer" value="3" label="Maximal charge that should be assumed for precursor peaks" help="(-max_charge) "/>
+      <param name="param_intensity_threshold" type="float" value="-1.0" label="Intensity threshold value for isotope wavelet feature finder, please look at the documentation of the class for details" help="(-intensity_threshold) "/>
+      <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>Corrects the precursor entries of MS/MS spectra, by using MS1 information.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorMassCorrector.html</help>
+</tool>