comparison NovorAdapter.xml @ 0:562d46a2f8b6 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:40:35 -0400
parents
children 16fcd0ea9937
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-1:000000000000 0:562d46a2f8b6
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.-->
3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="NovorAdapter" name="NovorAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Template for Tool creation</description>
6 <macros>
7 <token name="@EXECUTABLE@">NovorAdapter</token>
8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros>
12 <expand macro="requirements"/>
13 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@
16 #import re
17
18 ## Preprocessing
19 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir out &&
22 #if $novorFile:
23 mkdir novorFile &&
24 ln -s '$novorFile' 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)' &&
25 #end if
26
27 ## Main program call
28
29 set -o pipefail &&
30 @EXECUTABLE@ -write_ctd ./ &&
31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
33 -in
34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
35 -out
36 'out/output.${gxy2omsext("idxml")}'
37 #if $novorFile:
38 -novorFile
39 'novorFile/${re.sub("[^\w\-_]", "_", $novorFile.element_identifier)}.$gxy2omsext($novorFile.ext)'
40 #end if
41
42 ## Postprocessing
43 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
44 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
45 && mv '@EXECUTABLE@.ctd' '$ctd_out'
46 #end if]]></command>
47 <configfiles>
48 <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>
50 </configfiles>
51 <inputs>
52 <param name="in" 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="">
54 <option value="Trypsin" selected="true">Trypsin</option>
55 <expand macro="list_string_san"/>
56 </param>
57 <param name="fragmentation" argument="-fragmentation" display="radio" type="select" optional="false" label="Fragmentation method" help="">
58 <option value="CID" selected="true">CID</option>
59 <option value="HCD">HCD</option>
60 <expand macro="list_string_san"/>
61 </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)">
63 <option value="Trap" selected="true">Trap</option>
64 <option value="TOF">TOF</option>
65 <option value="FT">FT</option>
66 <expand macro="list_string_san"/>
67 </param>
68 <param name="fragment_mass_tolerance" 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=""/>
70 <param name="precursor_error_units" argument="-precursor_error_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
71 <option value="ppm" selected="true">ppm</option>
72 <option value="Da">Da</option>
73 <expand macro="list_string_san"/>
74 </param>
75 <param name="variable_modifications" 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>
78 <option value="Acetyl (N-term)">Acetyl (N-term)</option>
79 <option value="Amidated (C-term)">Amidated (C-term)</option>
80 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
81 <option value="Biotin (K)">Biotin (K)</option>
82 <option value="Biotin (N-term)">Biotin (N-term)</option>
83 <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
84 <option value="Carbamyl (K)">Carbamyl (K)</option>
85 <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
86 <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
87 <option value="Deamidated (NQ)">Deamidated (NQ)</option>
88 <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
89 <option value="Dioxidation (M)">Dioxidation (M)</option>
90 <option value="Methyl (C-term)">Methyl (C-term)</option>
91 <option value="Methyl (DE)">Methyl (DE)</option>
92 <option value="Oxidation (M)">Oxidation (M)</option>
93 <option value="Oxidation (HW)">Oxidation (HW)</option>
94 <option value="Phospho (ST)">Phospho (ST)</option>
95 <option value="Phospho (Y)">Phospho (Y)</option>
96 <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
97 <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
98 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
99 <option value="Sodium (C-term)">Sodium (C-term)</option>
100 <option value="Sodium (DE)">Sodium (DE)</option>
101 <option value="Sulfo (STY)">Sulfo (STY)</option>
102 <option value="Trimethyl (RK)">Trimethyl (RK)</option>
103 <expand macro="list_string_san"/>
104 </param>
105 <param name="fixed_modifications" 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>
108 <option value="Acetyl (N-term)">Acetyl (N-term)</option>
109 <option value="Amidated (C-term)">Amidated (C-term)</option>
110 <option value="Ammonia-loss (N-term C)">Ammonia-loss (N-term C)</option>
111 <option value="Biotin (K)">Biotin (K)</option>
112 <option value="Biotin (N-term)">Biotin (N-term)</option>
113 <option value="Carbamidomethyl (C)">Carbamidomethyl (C)</option>
114 <option value="Carbamyl (K)">Carbamyl (K)</option>
115 <option value="Carbamyl (N-term)">Carbamyl (N-term)</option>
116 <option value="Carboxymethyl (C)">Carboxymethyl (C)</option>
117 <option value="Deamidated (NQ)">Deamidated (NQ)</option>
118 <option value="Dehydrated (N-term C)">Dehydrated (N-term C)</option>
119 <option value="Dioxidation (M)">Dioxidation (M)</option>
120 <option value="Methyl (C-term)">Methyl (C-term)</option>
121 <option value="Methyl (DE)">Methyl (DE)</option>
122 <option value="Oxidation (M)">Oxidation (M)</option>
123 <option value="Oxidation (HW)">Oxidation (HW)</option>
124 <option value="Phospho (ST)">Phospho (ST)</option>
125 <option value="Phospho (Y)">Phospho (Y)</option>
126 <option value="Pyro-carbamidomethyl (N-term C)">Pyro-carbamidomethyl (N-term C)</option>
127 <option value="Pyro-Glu (E)">Pyro-Glu (E)</option>
128 <option value="Pyro-Glu (Q)">Pyro-Glu (Q)</option>
129 <option value="Sodium (C-term)">Sodium (C-term)</option>
130 <option value="Sodium (DE)">Sodium (DE)</option>
131 <option value="Sulfo (STY)">Sulfo (STY)</option>
132 <option value="Trimethyl (RK)">Trimethyl (RK)</option>
133 <expand macro="list_string_san"/>
134 </param>
135 <param name="forbiddenResidues" argument="-forbiddenResidues" multiple="true" type="select" optional="true" label="Forbidden Resiudes" help="">
136 <option value="">default (nothing chosen)</option>
137 <option value="I">I</option>
138 <option value="U">U</option>
139 <expand macro="list_string_san"/>
140 </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)"/>
142 <expand macro="adv_opts_macro">
143 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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="">
145 <expand macro="list_string_san"/>
146 </param>
147 </expand>
148 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
149 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
150 </param>
151 </inputs>
152 <outputs>
153 <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">
155 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
156 </data>
157 </outputs>
158 <tests>
159 <expand macro="autotest_NovorAdapter"/>
160 <expand macro="manutest_NovorAdapter"/>
161 </tests>
162 <help><![CDATA[Template for Tool creation
163
164
165 For more information, visit http://www.openms.de/documentation/UTILS_NovorAdapter.html]]></help>
166 <expand macro="references"/>
167 </tool>