Mercurial > repos > galaxyp > openms_compnovo
comparison PepNovoAdapter.patch @ 12:77d92924bb5a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 12:54:28 +0000 |
| parents | |
| children |
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| 11:00a6c0493f91 | 12:77d92924bb5a |
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| 1 --- PepNovoAdapter.xml 2020-05-12 15:55:24.712831518 +0200 | |
| 2 +++ /tmp/PepNovoAdapter.xml 2020-05-12 15:36:31.267276757 +0200 | |
| 3 @@ -42,8 +42,13 @@ | |
| 4 </configfiles> | |
| 5 <inputs> | |
| 6 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> | |
| 7 - <param name="model_directory" argument="-model_directory" type="text" optional="false" value="" label="Name of the directory where the model files are kept" help=""> | |
| 8 - <expand macro="list_string_san"/> | |
| 9 + <param name="model_directory" argument="-model_directory" type="select" optional="false" label="Name of the directory where the model files are kept" help=""> | |
| 10 + <options from_data_table="pepnovo_models"> | |
| 11 + <column name="name" index="0"/> | |
| 12 + <column name="value" index="2"/> | |
| 13 + <filter type="unique_value" name="unique_set" column="0"/> | |
| 14 + <validator type="no_options" message="No model directory available"/> | |
| 15 + </options> | |
| 16 </param> | |
| 17 <param name="correct_pm" argument="-correct_pm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Find optimal precursor mass and charge values" help=""/> | |
| 18 <param name="use_spectrum_charge" argument="-use_spectrum_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not correct charge" help=""/> | |
| 19 @@ -51,8 +56,14 @@ | |
| 20 <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=""/> | |
| 21 <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)"/> | |
| 22 <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)"/> | |
| 23 - <param name="model" argument="-model" type="text" optional="true" value="CID_IT_TRYP" label="Name of the model that should be used" help=""> | |
| 24 - <expand macro="list_string_san"/> | |
| 25 + <param name="model" argument="-model" type="select" label="Name of the model that should be used" help=""> | |
| 26 + <options from_data_table="pepnovo_models"> | |
| 27 + <column name="name" index="1"/> | |
| 28 + <column name="value" index="1"/> | |
| 29 + <filter type="param_value" ref="model_directory" column="2"/> | |
| 30 + <filter type="unique_value" column="1"/> | |
| 31 + <validator type="no_options" message="No model available"/> | |
| 32 + </options> | |
| 33 </param> | |
| 34 <param name="digest" argument="-digest" display="radio" type="select" optional="false" label="Enzyme used for digestion (default TRYPSIN)" help=""> | |
| 35 <option value="TRYPSIN" selected="true">TRYPSIN</option> |