comparison PepNovoAdapter.patch @ 11:36c84cb92e46 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:54:16 -0400
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10:9cc4b157e2fb 11:36c84cb92e46
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>