diff MRMMapper.xml @ 0:3d84209d3178 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MRMMapper.xml	Fri Oct 10 18:20:03 2014 -0400
@@ -0,0 +1,39 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="MRMMapper" name="MRMMapper" version="1.12.0">
+  <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
+  <macros>
+    <token name="@EXECUTABLE@">MRMMapper</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>MRMMapper
+
+-in ${param_in}
+-tr ${param_tr}
+-out ${param_out}
+-precursor_tolerance ${param_precursor_tolerance}
+-product_tolerance ${param_product_tolerance}
+${param_no-strict}
+-threads \${GALAXY_SLOTS:-24} 
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzML" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in)"/>
+    <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/>
+    <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance)"/>
+    <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance)"/>
+    <param name="param_no-strict" type="boolean" truevalue="-no-strict true" falsevalue="-no-strict false" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped." help="(-no-strict)"/>
+  </inputs>
+  <outputs>
+    <data name="param_out" label="Output file containing mapped chromatograms" format="mzML"/>
+  </outputs>
+  <help>**What it does**
+
+MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html
+
+@REFERENCES@
+</help>
+</tool>