diff PepNovoAdapter.patch @ 13:1cae2aac2260 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- a/PepNovoAdapter.patch	Fri Nov 06 20:38:59 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
---- 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>