diff idxml_to_tabular.xml @ 0:ba86fd127f5a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/idxml_to_tabular.xml	Wed Dec 19 00:32:25 2012 -0500
@@ -0,0 +1,48 @@
+<tool id="openms_idxml_to_tabular" version="0.1.0" name="Export idXML to Tabular">
+  <description>
+    Converts identification engine file formats.
+  </description>
+  <requirements>
+    <requirement type="package">openms</requirement>
+  </requirements>
+  <command interpreter="python">
+    openms_wrapper.py --executable 'TextExporter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${in}
+out=${out}
+#if $dump_type == "protein"
+proteins_only=true
+#end if
+#if $dump_type == "pepetide"
+peptides_only=true
+#end if
+$extra_rt
+</configfile>
+  </configfiles>
+  <inputs>
+    <param format="idxml" name="in" type="data" label="Input Identification File"/>
+    <param name="dump_type" type="select" label="Export type">
+      <option value="all">Run, peptide, and protein information</option>
+      <option value="protein">Run and protein information only</option>
+      <option value="peptide">Peptide information only</option>
+    </param>
+    <param name="extra_rt" type="boolean" truevalue="first_dim_rt=true" falsevalue="" label="Include RT information (if present)" />
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out">
+    </data>
+  </outputs>
+  <help>
+**What it does**
+
+Converts idXML files to tabular.
+
+**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>