comparison NovorAdapter.xml @ 6:fa544e12732f draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:45:52 +0000
parents 34dda034b019
children
comparison
equal deleted inserted replaced
5:34dda034b019 6:fa544e12732f
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Identification of Proteins/Peptides (SearchEngines)]-->
4 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Performs de novo sequencing of peptides from MS/MS data with Novor.</description> 4 <description>Performs de novo sequencing of peptides from MS/MS data with Novor</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">NovorAdapter</token> 6 <token name="@EXECUTABLE@">NovorAdapter</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $novorFile: 19 #if $novorFile:
21 mkdir novorFile && 20 mkdir novorFile &&
22 ln -s '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' && 21 cp '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
23 #end if 22 #end if
24 23
25 ## Main program call 24 ## Main program call
26 25
27 set -o pipefail && 26 set -o pipefail &&
45 <configfiles> 44 <configfiles>
46 <inputs name="args_json" data_style="paths"/> 45 <inputs name="args_json" data_style="paths"/>
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> 46 <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>
48 </configfiles> 47 </configfiles>
49 <inputs> 48 <inputs>
50 <param argument="-in" type="data" format="mzml" optional="false" label="MzML Input file" help=" select mzml data sets(s)"/> 49 <param argument="-in" type="data" format="mzml" label="MzML Input file" help=" select mzml data sets(s)"/>
51 <param argument="-enzyme" type="select" optional="true" label="Digestion enzyme - currently only Trypsin is supported" help=""> 50 <param argument="-enzyme" type="select" label="Digestion enzyme - currently only Trypsin is supported" help="">
52 <option value="Trypsin" selected="true">Trypsin</option> 51 <option value="Trypsin" selected="true">Trypsin</option>
53 <expand macro="list_string_san" name="enzyme"/> 52 <expand macro="list_string_san" name="enzyme"/>
54 </param> 53 </param>
55 <param argument="-fragmentation" type="select" optional="true" label="Fragmentation method" help=""> 54 <param argument="-fragmentation" type="select" label="Fragmentation method" help="">
56 <option value="CID" selected="true">CID</option> 55 <option value="CID" selected="true">CID</option>
57 <option value="HCD">HCD</option> 56 <option value="HCD">HCD</option>
58 <expand macro="list_string_san" name="fragmentation"/> 57 <expand macro="list_string_san" name="fragmentation"/>
59 </param> 58 </param>
60 <param argument="-massAnalyzer" type="select" optional="true" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)"> 59 <param argument="-massAnalyzer" type="select" label="MassAnalyze" help="e.g. (Oritrap CID-Trap, CID-FT, HCD-FT; QTof CID-TOF)">
61 <option value="Trap" selected="true">Trap</option> 60 <option value="Trap" selected="true">Trap</option>
62 <option value="TOF">TOF</option> 61 <option value="TOF">TOF</option>
63 <option value="FT">FT</option> 62 <option value="FT">FT</option>
64 <expand macro="list_string_san" name="massAnalyzer"/> 63 <expand macro="list_string_san" name="massAnalyzer"/>
65 </param> 64 </param>
66 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Fragmentation error tolerance (Da)" help=""/> 65 <param argument="-fragment_mass_tolerance" type="float" value="0.5" label="Fragmentation error tolerance (Da)" help=""/>
67 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="15.0" label="Precursor error tolerance (ppm or Da)" help=""/> 66 <param argument="-precursor_mass_tolerance" type="float" value="15.0" label="Precursor error tolerance (ppm or Da)" help=""/>
68 <param argument="-precursor_error_units" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> 67 <param argument="-precursor_error_units" type="select" label="Unit of precursor mass tolerance" help="">
69 <option value="ppm" selected="true">ppm</option> 68 <option value="ppm" selected="true">ppm</option>
70 <option value="Da">Da</option> 69 <option value="Da">Da</option>
71 <expand macro="list_string_san" name="precursor_error_units"/> 70 <expand macro="list_string_san" name="precursor_error_units"/>
72 </param> 71 </param>
73 <param argument="-variable_modifications" multiple="true" type="select" optional="true" label="Variable modifications" help=""> 72 <param argument="-variable_modifications" type="select" multiple="true" optional="true" label="Variable modifications" help="">
74 <option value="Acetyl (K)">Acetyl (K)</option> 73 <option value="Acetyl (K)">Acetyl (K)</option>
75 <option value="Acetyl (N-term)">Acetyl (N-term)</option> 74 <option value="Acetyl (N-term)">Acetyl (N-term)</option>
76 <option value="Amidated (C-term)">Amidated (C-term)</option> 75 <option value="Amidated (C-term)">Amidated (C-term)</option>
77 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option> 76 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
78 <option value="Biotin (K)">Biotin (K)</option> 77 <option value="Biotin (K)">Biotin (K)</option>
97 <option value="Sodium (DE)">Sodium (DE)</option> 96 <option value="Sodium (DE)">Sodium (DE)</option>
98 <option value="Sulfo (STY)">Sulfo (STY)</option> 97 <option value="Sulfo (STY)">Sulfo (STY)</option>
99 <option value="Trimethyl (RK)">Trimethyl (RK)</option> 98 <option value="Trimethyl (RK)">Trimethyl (RK)</option>
100 <expand macro="list_string_san" name="variable_modifications"/> 99 <expand macro="list_string_san" name="variable_modifications"/>
101 </param> 100 </param>
102 <param argument="-fixed_modifications" multiple="true" type="select" optional="true" label="Fixed modifications" help=""> 101 <param argument="-fixed_modifications" type="select" multiple="true" optional="true" label="Fixed modifications" help="">
103 <option value="Acetyl (K)">Acetyl (K)</option> 102 <option value="Acetyl (K)">Acetyl (K)</option>
104 <option value="Acetyl (N-term)">Acetyl (N-term)</option> 103 <option value="Acetyl (N-term)">Acetyl (N-term)</option>
105 <option value="Amidated (C-term)">Amidated (C-term)</option> 104 <option value="Amidated (C-term)">Amidated (C-term)</option>
106 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option> 105 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
107 <option value="Biotin (K)">Biotin (K)</option> 106 <option value="Biotin (K)">Biotin (K)</option>
126 <option value="Sodium (DE)">Sodium (DE)</option> 125 <option value="Sodium (DE)">Sodium (DE)</option>
127 <option value="Sulfo (STY)">Sulfo (STY)</option> 126 <option value="Sulfo (STY)">Sulfo (STY)</option>
128 <option value="Trimethyl (RK)">Trimethyl (RK)</option> 127 <option value="Trimethyl (RK)">Trimethyl (RK)</option>
129 <expand macro="list_string_san" name="fixed_modifications"/> 128 <expand macro="list_string_san" name="fixed_modifications"/>
130 </param> 129 </param>
131 <param argument="-forbiddenResidues" display="checkboxes" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help=""> 130 <param argument="-forbiddenResidues" type="select" multiple="true" optional="true" label="Forbidden Resiudes" help="">
132 <option value="I">I</option> 131 <option value="I">I</option>
133 <option value="U">U</option> 132 <option value="U">U</option>
134 <expand macro="list_string_san" name="forbiddenResidues"/> 133 <expand macro="list_string_san" name="forbiddenResidues"/>
135 </param> 134 </param>
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)"/> 135 <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)"/>
137 <expand macro="adv_opts_macro"> 136 <expand macro="adv_opts_macro">
138 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 137 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
139 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 138 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
140 <expand macro="list_string_san" name="test"/> 139 <expand macro="list_string_san" name="test"/>
141 </param> 140 </param>
142 </expand> 141 </expand>
143 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 142 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
144 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 143 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
148 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 147 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 148 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 149 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data> 150 </data>
152 </outputs> 151 </outputs>
153 <tests><!-- TOPP_NovorAdapter_1 --> 152 <tests>
153 <!-- TOPP_NovorAdapter_1 -->
154 </tests> 154 </tests>
155 <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor. 155 <help><![CDATA[Performs de novo sequencing of peptides from MS/MS data with Novor.
156 156
157 157
158 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NovorAdapter.html]]></help> 158 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NovorAdapter.html]]></help>
159 <expand macro="references"/> 159 <expand macro="references"/>
160 </tool> 160 </tool>