diff PrecursorMassCorrector.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PrecursorMassCorrector.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,43 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="PrecursorMassCorrector" name="PrecursorMassCorrector" version="1.12.0">
+  <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="stdio"/>
+  <expand macro="requirements"/>
+  <command>PrecursorMassCorrector
+
+-in ${param_in}
+-out ${param_out}
+-feature_in ${param_feature_in}
+-precursor_mass_tolerance ${param_precursor_mass_tolerance}
+-threads \${GALAXY_SLOTS:-24} 
+#if $adv_opts.adv_opts_selector=='advanced':
+    -max_charge ${adv_opts.param_max_charge}
+    -intensity_threshold ${adv_opts.param_intensity_threshold}
+#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 #br#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;#br#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)"/>
+    </expand>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output mzML file." format="mzML"/>
+  </outputs>
+  <help>**What it does**
+
+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
+
+@REFERENCES@
+</help>
+</tool>