diff xtandem_adapter.xml @ 2:cf0d72c7b482 draft

Update.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xtandem_adapter.xml	Fri May 10 17:31:05 2013 -0400
@@ -0,0 +1,94 @@
+<tool id="xtandem_adapter" version="0.1.0" name="X! Tandem (OpenMS)">
+  <description>
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <expand macro="requires">
+    <requirement type="package">tandem</requirement>
+  </expand>
+  <command interpreter="python">
+    openms_wrapper.py 
+    --executable 'XTandemAdapter' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=$input1
+out=$out
+database=$database
+xtandem_executable=@WHICH(tandem)@
+variable_modifications=${variable_modifications or ''}
+fixed_modifications=${fixed_modifications or ''}
+precursor_mass_tolerance=$precursor_mass_tolerance
+precursor_error_units=$precursor_mass_tolerance_unit
+fragment_mass_tolerance=$fragment_mass_tolerance
+fragment_error_units=$fragment_mass_tolerance_unit
+min_precursor_charge=$min_precursor_charge
+max_precursor_charge=$max_precursor_charge
+cleavage_site=$cleavage_site
+minimum_fragment_mz=$minimum_fragment_mz
+max_valid_expect=$max_valid_expect
+refinement=$refinement
+semi_cleavage=$semi_cleavage
+</configfile>
+  </configfiles>
+  <inputs>
+    <expand macro="id_inputs" />
+    <expand macro="fixed_modifications_param" />
+    <expand macro="variable_modifications_param" />
+    <expand macro="precursor_mass_tolerance_param" />
+    <expand macro="precursor_mass_tolerance_unit_param" />
+    <expand macro="fragment_mass_tolerance_param" />
+    <expand macro="fragment_mass_tolerance_unit_param" />
+    <expand macro="precursor_charge_params" />
+    <param name="cleavage_site" label="Cleavage Site" type="select">
+      <option value="[R]|{P}">argc</option>
+      <option value="[X]|[D]">aspn</option>
+      <option value="[FMWY]|{P}">chymotrypsin</option>
+      <option value="[R]|[X]">clostripain</option>
+      <option value="[M]|{P}">cnbr</option>
+      <option value="[AGILV]|{P}">elastase</option>
+      <option value="[D]|{P}">formicacid</option>
+      <option value="[DE]|{P}">gluc</option>
+      <option value="[E]|{P}">gluc_bicarb</option>
+      <option value="[W]|[X]">iodosobenzoate</option>
+      <option value="[K]|[P]">lysc</option>
+      <option value="[K]|[X]">lysc-p</option>
+      <option value="[X]|[K]">lysn</option>
+      <option value="[X]|[AKRS]">lysn_promisc</option>
+      <option value="[X]|[X]">nonspecific</option>
+      <option value="[FL]|[X]">pepsina</option>
+      <option value="[P]|[X]">protein_endopeptidase</option>
+      <option value="[E]|[X]">staph_protease</option>
+      <option value="[KR]|{P}" selected="true">trypsin</option>
+      <option value="[DEKR]|{P}">trypsin_gluc</option>
+      <option value="[K]|{P}">trypsin_k</option>
+      <option value="[R]|{P}">trypsin_r</option>
+      <sanitizer>
+        <valid>
+          <add value="{"/>
+          <add value="}"/>
+          <add value="|"/>
+          <add value="["/>
+          <add value="]"/>
+        </valid>
+      </sanitizer>      
+    </param>
+    <param name="minimum_fragment_mz" label="Minimum Fragment m/z" value="150" type="float" />
+    <param name="max_valid_expect" label="Maximum Valid E-Value to be Reported" value=".1" type="float" />
+    <param name="semi_cleavage" type="boolean" label="Enable Semi-Cleavage" checked="false" truevalue="true" falsevalue="false" help="If set, both termini must NOT follow the cutting rule. For most applications it is NOT recommended to set this flag." />
+    <param name="refinement" type="boolean" label="Enable Refinement" checked="false" truevalue="true" falsevalue="false" help="Enable the refinement. For most applications (especially when using FDR, PEP approaches) it is NOT recommended to set this flag." />
+  </inputs>
+  <expand macro="id_outputs" />
+  <help>
+**What it does**
+
+
+**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.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+  </help>
+</tool>