annotate PepNovoAdapter.patch @ 11:2c6f5858e89a draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

--- 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>