Mercurial > repos > galaxyp > openms_cometadapter
view PepNovoAdapter.patch @ 5:67b02e52296a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"
author | galaxyp |
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date | Thu, 24 Sep 2020 12:14:52 +0000 |
parents | 2ffc94cb0766 |
children |
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--- PepNovoAdapter.xml 2020-05-12 15:55:24.712831518 +0200 +++ /tmp/PepNovoAdapter.xml 2020-05-12 15:36:31.267276757 +0200 @@ -42,8 +42,13 @@ </configfiles> <inputs> <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> - <param name="model_directory" argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help=""> - <expand macro="list_string_san"/> + <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> + <options from_data_table="pepnovo_models"> + <column name="name" index="0"/> + <column name="value" index="2"/> + <filter type="unique_value" name="unique_set" column="0"/> + <validator type="no_options" message="No model directory available"/> + </options> </param> <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> @@ -51,8 +56,14 @@ <param name="no_quality_filter" argument="-no_quality_filter" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not remove low quality spectra" help=""/> <param name="fragment_tolerance" argument="-fragment_tolerance" type="float" optional="true" value="-1.0" label="The fragment tolerance (between 0 and 0.75 Da" help="Set to -1.0 to use model's default setting)"/> <param name="pm_tolerance" argument="-pm_tolerance" type="float" optional="true" value="-1.0" label="The precursor mass tolerance (between 0 and 5.0 Da" help="Set to -1.0 to use model's default setting)"/> - <param name="model" argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help=""> - <expand macro="list_string_san"/> + <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> + <options from_data_table="pepnovo_models"> + <column name="name" index="1"/> + <column name="value" index="1"/> + <filter type="param_value" ref="model_directory" column="2"/> + <filter type="unique_value" column="1"/> + <validator type="no_options" message="No model available"/> + </options> </param> <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> <option value="TRYPSIN" selected="true">TRYPSIN</option>