diff id_filter.xml @ 2:cf0d72c7b482 draft

Update.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/id_filter.xml	Fri May 10 17:31:05 2013 -0400
@@ -0,0 +1,48 @@
+<tool id="openms_id_filter" version="0.1.0" name="ID Filter">
+  <description>
+    Filters protein identification engine results by different criteria.
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <expand macro="requires" />
+  <command interpreter="python">
+    openms_wrapper.py --executable 'IDFilter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=$input1
+out=$output
+score!pep=$peptide_score
+score!prot=$protein_score
+thresh!pep=$peptide_threshold
+thresh!prot=$protein_threshold
+best!n_peptide_hits=$n_peptide_hits
+best!n_protein_hits=$n_protein_hits
+</configfile>
+  </configfiles>
+  <inputs>
+    <param name="input1" label="Input" type="data" format="idxml" />
+    <param name="n_peptide_hits" label="Keep only the 'n' highest scoring peptide hits per spectrum (for n>0). " value="0" type="integer" />
+    <param name="n_protein_hits" label="Keep only the 'n' highest scoring protein hits per spectrum (for n>0). " value="0" type="integer" />
+    <param name="peptide_score" label="Peptide Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" />
+    <param name="protein_score" label="Protein Score. " value="0" type="float" help="The score which should be reached by a peptide hit to be kept. The score is dependent on the most recent(!) preprocessing - it could be Mascot scores (if a MascotAdapter was applied before), or an FDR (if FalseDiscoveryRate was applied before), etc. (default: '0')" />
+    <param name="peptide_threshold" label="Peptide Threshold" help="Keep a peptide hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" />
+    <param name="protein_threshold" label="Protein Threshold" help="Keep a protein hit only if its score is above this fraction of the peptide significance threshold." value="0" type="float" />
+  </inputs>
+  <outputs>
+    <data format="idxml" name="output" />
+  </outputs>
+  <help>
+**What it does**
+
+This tool is used to filter the identifications found by a peptide/protein identification tool like Mascot. Different filters can be applied.
+
+**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>