Mercurial > repos > galaxyp > openms_novoradapter
comparison NovorAdapter.xml @ 5:34dda034b019 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:20:30 +0000 |
parents | 031adfb7fce0 |
children | fa544e12732f |
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4:031adfb7fce0 | 5:34dda034b019 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Utilities]--> | 3 <!--Proposed Tool Section: [Utilities]--> |
4 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy1" profile="20.05"> | 4 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Template for Tool creation</description> | 5 <description>Performs de novo sequencing of peptides from MS/MS data with Novor.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">NovorAdapter</token> | 7 <token name="@EXECUTABLE@">NovorAdapter</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 <import>macros_autotest.xml</import> | |
10 <import>macros_test.xml</import> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
47 <configfiles> | 45 <configfiles> |
48 <inputs name="args_json" data_style="paths"/> | 46 <inputs name="args_json" data_style="paths"/> |
49 <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 47 <configfile name="hardcoded_json"><![CDATA[{"executable": "/home/berntm/Downloads/novor/lib/novor.jar", "java_executable": "java", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
50 </configfiles> | 48 </configfiles> |
51 <inputs> | 49 <inputs> |
52 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/> | 50 <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/> |
53 <param name="enzyme" argument="-enzyme" display="radio" type="select" optional="false" label="Digestion enzyme - currently only Trypsin is supported" help=""> | 51 <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme - currently only Trypsin is supported" help=""> |
54 <option value="Trypsin" selected="true">Trypsin</option> | 52 <option value="Trypsin" selected="true">Trypsin</option> |
55 <expand macro="list_string_san"/> | 53 <expand macro="list_string_san" name="enzyme"/> |
56 </param> | 54 </param> |
57 <param name="fragmentation" argument="-fragmentation" display="radio" type="select" optional="false" label="Fragmentation method" help=""> | 55 <param argument="-fragmentation" type="select" optional="true" label="Fragmentation method" help=""> |
58 <option value="CID" selected="true">CID</option> | 56 <option value="CID" selected="true">CID</option> |
59 <option value="HCD">HCD</option> | 57 <option value="HCD">HCD</option> |
60 <expand macro="list_string_san"/> | 58 <expand macro="list_string_san" name="fragmentation"/> |
61 </param> | 59 </param> |
62 <param name="massAnalyzer" argument="-massAnalyzer" display="radio" type="select" optional="false" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)"> | 60 <param argument="-massAnalyzer" type="select" optional="true" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)"> |
63 <option value="Trap" selected="true">Trap</option> | 61 <option value="Trap" selected="true">Trap</option> |
64 <option value="TOF">TOF</option> | 62 <option value="TOF">TOF</option> |
65 <option value="FT">FT</option> | 63 <option value="FT">FT</option> |
66 <expand macro="list_string_san"/> | 64 <expand macro="list_string_san" name="massAnalyzer"/> |
67 </param> | 65 </param> |
68 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance (Da)" help=""/> | 66 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance (Da)" help=""/> |
69 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance (ppm or Da)" help=""/> | 67 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance (ppm or Da)" help=""/> |
70 <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> | 68 <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> |
71 <option value="ppm" selected="true">ppm</option> | 69 <option value="ppm" selected="true">ppm</option> |
72 <option value="Da">Da</option> | 70 <option value="Da">Da</option> |
73 <expand macro="list_string_san"/> | 71 <expand macro="list_string_san" name="precursor_error_units"/> |
74 </param> | 72 </param> |
75 <param name="variable_modifications" argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help=""> | 73 <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help=""> |
76 <option value="">default (nothing chosen)</option> | |
77 <option value="Acetyl (K)">Acetyl (K)</option> | 74 <option value="Acetyl (K)">Acetyl (K)</option> |
78 <option value="Acetyl (N-term)">Acetyl (N-term)</option> | 75 <option value="Acetyl (N-term)">Acetyl (N-term)</option> |
79 <option value="Amidated (C-term)">Amidated (C-term)</option> | 76 <option value="Amidated (C-term)">Amidated (C-term)</option> |
80 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option> | 77 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option> |
81 <option value="Biotin (K)">Biotin (K)</option> | 78 <option value="Biotin (K)">Biotin (K)</option> |
98 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option> | 95 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option> |
99 <option value="Sodium (C-term)">Sodium (C-term)</option> | 96 <option value="Sodium (C-term)">Sodium (C-term)</option> |
100 <option value="Sodium (DE)">Sodium (DE)</option> | 97 <option value="Sodium (DE)">Sodium (DE)</option> |
101 <option value="Sulfo (STY)">Sulfo (STY)</option> | 98 <option value="Sulfo (STY)">Sulfo (STY)</option> |
102 <option value="Trimethyl (RK)">Trimethyl (RK)</option> | 99 <option value="Trimethyl (RK)">Trimethyl (RK)</option> |
103 <expand macro="list_string_san"/> | 100 <expand macro="list_string_san" name="variable_modifications"/> |
104 </param> | 101 </param> |
105 <param name="fixed_modifications" argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help=""> | 102 <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help=""> |
106 <option value="">default (nothing chosen)</option> | |
107 <option value="Acetyl (K)">Acetyl (K)</option> | 103 <option value="Acetyl (K)">Acetyl (K)</option> |
108 <option value="Acetyl (N-term)">Acetyl (N-term)</option> | 104 <option value="Acetyl (N-term)">Acetyl (N-term)</option> |
109 <option value="Amidated (C-term)">Amidated (C-term)</option> | 105 <option value="Amidated (C-term)">Amidated (C-term)</option> |
110 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option> | 106 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option> |
111 <option value="Biotin (K)">Biotin (K)</option> | 107 <option value="Biotin (K)">Biotin (K)</option> |
128 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option> | 124 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option> |
129 <option value="Sodium (C-term)">Sodium (C-term)</option> | 125 <option value="Sodium (C-term)">Sodium (C-term)</option> |
130 <option value="Sodium (DE)">Sodium (DE)</option> | 126 <option value="Sodium (DE)">Sodium (DE)</option> |
131 <option value="Sulfo (STY)">Sulfo (STY)</option> | 127 <option value="Sulfo (STY)">Sulfo (STY)</option> |
132 <option value="Trimethyl (RK)">Trimethyl (RK)</option> | 128 <option value="Trimethyl (RK)">Trimethyl (RK)</option> |
133 <expand macro="list_string_san"/> | 129 <expand macro="list_string_san" name="fixed_modifications"/> |
134 </param> | 130 </param> |
135 <param name="forbiddenResidues" argument="-forbiddenResidues" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help=""> | 131 <param argument="-forbiddenResidues" display="checkboxes" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help=""> |
136 <option value="">default (nothing chosen)</option> | |
137 <option value="I">I</option> | 132 <option value="I">I</option> |
138 <option value="U">U</option> | 133 <option value="U">U</option> |
139 <expand macro="list_string_san"/> | 134 <expand macro="list_string_san" name="forbiddenResidues"/> |
140 </param> | 135 </param> |
141 <param name="novorFile" argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/> | 136 <param argument="-novorFile" type="data" format="txt" optional="true" label="File to introduce customized algorithm parameters for advanced users (otional .novor file)" help=" select txt data sets(s)"/> |
142 <expand macro="adv_opts_macro"> | 137 <expand macro="adv_opts_macro"> |
143 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 138 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
144 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 139 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
145 <expand macro="list_string_san"/> | 140 <expand macro="list_string_san" name="test"/> |
146 </param> | 141 </param> |
147 </expand> | 142 </expand> |
148 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 143 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
149 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 144 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
150 </param> | 145 </param> |
153 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> | 148 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> |
154 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
155 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
156 </data> | 151 </data> |
157 </outputs> | 152 </outputs> |
158 <tests> | 153 <tests><!-- TOPP_NovorAdapter_1 --> |
159 <expand macro="autotest_NovorAdapter"/> | |
160 <expand macro="manutest_NovorAdapter"/> | |
161 </tests> | 154 </tests> |
162 <help><![CDATA[Template for Tool creation | 155 <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor. |
163 | 156 |
164 | 157 |
165 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_NovorAdapter.html]]></help> | 158 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NovorAdapter.html]]></help> |
166 <expand macro="references"/> | 159 <expand macro="references"/> |
167 </tool> | 160 </tool> |