diff peak_file_filter.xml @ 0:ba86fd127f5a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peak_file_filter.xml	Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,68 @@
+<tool id="openms_peak_file_filter" version="0.1.0" name="mzML File Filter">
+  <description>
+    Extract portions of peak lists.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'FileFilter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+#if $mz.specify
+mz=${mz.min}:${mz.max}
+#end if
+#if $rt.specify
+rt=${rt.min}:${rt.max}
+#end if
+#if $intensity.specify
+int=${intensity.min}:${intensity.max}
+#end if
+sn=${signal_to_noise}
+in=${in}
+in_type=mzML
+out=${out}
+out_type=mzML
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="mzml" name="in" type="data" label="Input mzML File"/>
+    <param type="float" name="signal_to_noise" label="Minimum signal-to-noise ratio" value="0" />
+    <conditional name="mz">
+      <param type="boolean" name="specify" label="Filter by m/z" />
+      <when value="true">
+        <param type="float" name="min" label="Minimum m/z (optional)" optional="true" value="" />
+        <param type="float" name="max" label="Maximum m/z (optional)" optional="true" value="" />
+      </when>
+    </conditional>
+    <conditional name="rt">
+      <param type="boolean" name="specify" label="Filter by retention time" />
+      <when value="true">
+        <param type="float" name="min" label="Minimum retention time (optional)" optional="true" value="" />
+        <param type="float" name="max" label="Maximum retention (optional)" optional="true" value="" />
+      </when>
+    </conditional>
+    <conditional name="intensity">
+      <param type="boolean" name="specify" label="Filter by intensity" />
+      <when value="true">
+        <param type="float" name="min" label="Minimum intensity (optional)" optional="true" value="" />
+        <param type="float" name="max" label="Maximum intensity (optional)" optional="true" value="" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="mzml" name="out" />
+  </outputs>
+  <help>
+**What it does**
+
+Extracts portions of the data from an mzML.
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+  </help>
+</tool>