Mercurial > repos > galaxyp > openms
diff xtandem_adapter.xml @ 2:cf0d72c7b482 draft
Update.
author | galaxyp |
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date | Fri, 10 May 2013 17:31:05 -0400 |
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--- /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>