Mercurial > repos > galaxyp > openms_cruxadapter

comparison CruxAdapter.xml @ 4:a915cadc2f07 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:08:43 +0000
parents aed7aeb6feec
children
comparison
equal deleted inserted replaced
3:ff40d13a0eb3 4:a915cadc2f07
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="CruxAdapter" name="CruxAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="CruxAdapter" name="CruxAdapter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Identifies MS/MS spectra using Crux.</description> 5 <description>Identifies MS/MS spectra using Crux.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">CruxAdapter</token> 7 <token name="@EXECUTABLE@">CruxAdapter</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@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"crux_executable": "crux", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"crux_executable": "crux", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/> 46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
49 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/> 47 <param argument="-database" type="data" format="fasta" optional="false" label="FASTA file" help=" select fasta data sets(s)"/>
50 <param name="extra_index_args" argument="-extra_index_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-index" help=""> 48 <param argument="-extra_index_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-index" help="">
51 <expand macro="list_string_san"/> 49 <expand macro="list_string_san" name="extra_index_args"/>
52 </param> 50 </param>
53 <param name="extra_search_args" argument="-extra_search_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-search" help=""> 51 <param argument="-extra_search_args" type="text" optional="true" value="" label="Extra arguments to be passed to tide-search" help="">
54 <expand macro="list_string_san"/> 52 <expand macro="list_string_san" name="extra_search_args"/>
55 </param> 53 </param>
56 <param name="extra_percolator_args" argument="-extra_percolator_args" type="text" optional="true" value="" label="Extra arguments to be passed to percolato" help=""> 54 <param argument="-extra_percolator_args" type="text" optional="true" value="" label="Extra arguments to be passed to percolato" help="">
57 <expand macro="list_string_san"/> 55 <expand macro="list_string_san" name="extra_percolator_args"/>
58 </param> 56 </param>
59 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)" help=""/> 57 <param argument="-precursor_mass_tolerance" type="float" optional="true" value="10.0" label="Precursor monoisotopic mass tolerance (Crux parameter: peptide_mass_tolerance)" help=""/>
60 <param name="precursor_mass_units" argument="-precursor_mass_units" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance (amu, m/z or ppm)" help=""> 58 <param argument="-precursor_mass_units" type="select" optional="true" label="Unit of precursor mass tolerance (amu, m/z or ppm)" help="">
61 <option value="mass">mass</option> 59 <option value="mass">mass</option>
62 <option value="mz">mz</option> 60 <option value="mz">mz</option>
63 <option value="ppm" selected="true">ppm</option> 61 <option value="ppm" selected="true">ppm</option>
64 <expand macro="list_string_san"/> 62 <expand macro="list_string_san" name="precursor_mass_units"/>
65 </param> 63 </param>
66 <param name="fragment_bin_offset" argument="-fragment_bin_offset" type="float" optional="true" value="0.0" label="In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0" help="(i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da)"/> 64 <param argument="-fragment_bin_offset" type="float" optional="true" value="0.0" label="In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0" help="(i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da)"/>
67 <param name="fragment_bin_width" argument="-fragment_bin_width" type="float" optional="true" value="0.02" label="Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized" help="This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended"/> 65 <param argument="-fragment_bin_width" type="float" optional="true" value="0.02" label="Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized" help="This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended"/>
68 <param name="isotope_error" argument="-isotope_error" type="text" optional="true" value="" label="List of positive, non-zero integers" help=""> 66 <param argument="-isotope_error" type="text" optional="true" value="" label="List of positive, non-zero integers" help="">
69 <expand macro="list_string_san"/> 67 <expand macro="list_string_san" name="isotope_error"/>
70 </param> 68 </param>
71 <param name="run_percolator" argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/> 69 <param argument="-run_percolator" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to run percolator after tide-search" help=""/>
72 <param name="enzyme" argument="-enzyme" type="select" optional="false" label="The enzyme used for peptide digestion" help=""> 70 <param argument="-enzyme" type="select" optional="true" label="The enzyme used for peptide digestion" help="">
73 <option value="custom-enzyme">custom-enzyme</option> 71 <option value="custom-enzyme">custom-enzyme</option>
72 <option value="pepsin-a">pepsin-a</option>
73 <option value="cyanogen-bromide">cyanogen-bromide</option>
74 <option value="clostripain">clostripain</option>
75 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
76 <option value="no-enzyme">no-enzyme</option>
74 <option value="arg-c">arg-c</option> 77 <option value="arg-c">arg-c</option>
75 <option value="asp-n">asp-n</option> 78 <option value="asp-n">asp-n</option>
76 <option value="iodosobenzoate">iodosobenzoate</option> 79 <option value="iodosobenzoate">iodosobenzoate</option>
77 <option value="staph-protease">staph-protease</option> 80 <option value="staph-protease">staph-protease</option>
78 <option value="proline-endopeptidase">proline-endopeptidase</option> 81 <option value="proline-endopeptidase">proline-endopeptidase</option>
79 <option value="glu-c">glu-c</option> 82 <option value="glu-c">glu-c</option>
80 <option value="pepsin-a">pepsin-a</option> 83 <option value="elastase">elastase</option>
81 <option value="cyanogen-bromide">cyanogen-bromide</option>
82 <option value="clostripain">clostripain</option>
83 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
84 <option value="no-enzyme">no-enzyme</option>
85 <option value="chymotrypsin">chymotrypsin</option> 84 <option value="chymotrypsin">chymotrypsin</option>
86 <option value="trypsin/p">trypsin/p</option>
87 <option value="elastase">elastase</option>
88 <option value="lys-c">lys-c</option> 85 <option value="lys-c">lys-c</option>
89 <option value="lys-n">lys-n</option> 86 <option value="lys-n">lys-n</option>
87 <option value="trypsin/p">trypsin/p</option>
90 <option value="trypsin" selected="true">trypsin</option> 88 <option value="trypsin" selected="true">trypsin</option>
91 <expand macro="list_string_san"/> 89 <expand macro="list_string_san" name="enzyme"/>
92 </param> 90 </param>
93 <param name="digestion" argument="-digestion" display="radio" type="select" optional="false" label="Full, partial or non specific digestion" help=""> 91 <param argument="-digestion" type="select" optional="true" label="Full, partial or non specific digestion" help="">
94 <option value="full-digest" selected="true">full-digest</option> 92 <option value="full-digest" selected="true">full-digest</option>
95 <option value="partial-digest">partial-digest</option> 93 <option value="partial-digest">partial-digest</option>
96 <option value="non-specific-digest">non-specific-digest</option> 94 <option value="non-specific-digest">non-specific-digest</option>
97 <expand macro="list_string_san"/> 95 <expand macro="list_string_san" name="digestion"/>
98 </param> 96 </param>
99 <param name="allowed_missed_cleavages" argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/> 97 <param argument="-allowed_missed_cleavages" type="integer" optional="true" value="0" label="Number of possible cleavage sites missed by the enzyme, maximum value is 5; for enzyme search" help=""/>
100 <param name="decoy_format" argument="-decoy_format" display="radio" type="select" optional="false" label="Decoy generation method either by reversing the sequence or shuffling it" help=""> 98 <param argument="-decoy_format" type="select" optional="true" label="Decoy generation method either by reversing the sequence or shuffling it" help="">
101 <option value="none">none</option> 99 <option value="none">none</option>
102 <option value="shuffle" selected="true">shuffle</option> 100 <option value="shuffle" selected="true">shuffle</option>
103 <option value="peptide-reverse">peptide-reverse</option> 101 <option value="peptide-reverse">peptide-reverse</option>
104 <option value="protein-reverse">protein-reverse</option> 102 <option value="protein-reverse">protein-reverse</option>
105 <expand macro="list_string_san"/> 103 <expand macro="list_string_san" name="decoy_format"/>
106 </param> 104 </param>
107 <param name="keep_terminal_aminos" argument="-keep_terminal_aminos" display="radio" type="select" optional="false" label="Whether to keep N and C terminal in place or also shuffled / reversed" help=""> 105 <param argument="-keep_terminal_aminos" type="select" optional="true" label="Whether to keep N and C terminal in place or also shuffled / reversed" help="">
108 <option value="N">N</option> 106 <option value="N">N</option>
109 <option value="C">C</option> 107 <option value="C">C</option>
110 <option value="NC" selected="true">NC</option> 108 <option value="NC" selected="true">NC</option>
111 <option value="none">none</option> 109 <option value="none">none</option>
112 <expand macro="list_string_san"/> 110 <expand macro="list_string_san" name="keep_terminal_aminos"/>
113 </param> 111 </param>
114 <param name="cterm_modifications" argument="-cterm_modifications" type="text" optional="true" value="" label="Specifies C-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = &lt;empty&gt;"> 112 <param argument="-cterm_modifications" type="text" optional="true" value="" label="Specifies C-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of C-terminal modification sequences of the form: X+21.9819 Default = &lt;empty&gt;">
115 <expand macro="list_string_san"/> 113 <expand macro="list_string_san" name="cterm_modifications"/>
116 </param> 114 </param>
117 <param name="nterm_modifications" argument="-nterm_modifications" type="text" optional="true" value="" label="Specifies N-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = &lt;empty&gt;"> 115 <param argument="-nterm_modifications" type="text" optional="true" value="" label="Specifies N-terminal static and variable mass modifications on peptides" help="Specify a comma-separated list of N-terminal modification sequences of the form: 1E-18.0106,C-17.0265 Default = &lt;empty&gt;">
118 <expand macro="list_string_san"/> 116 <expand macro="list_string_san" name="nterm_modifications"/>
119 </param> 117 </param>
120 <param name="modifications" argument="-modifications" type="text" optional="true" value="" label="Expression for static and variable mass modifications to include" help="Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146"> 118 <param argument="-modifications" type="text" optional="true" value="" label="Expression for static and variable mass modifications to include" help="Specify a comma-separated list of modification sequences of the form: C+57.02146,2M+15.9949,1STY+79.966331,... Default = C+57.02146">
121 <expand macro="list_string_san"/> 119 <expand macro="list_string_san" name="modifications"/>
122 </param> 120 </param>
123 <param name="test_fdr" argument="-test_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results" help=""/> 121 <param argument="-test_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results" help=""/>
124 <param name="train_fdr" argument="-train_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help=""/> 122 <param argument="-train_fdr" type="float" optional="true" value="0.01" label="False discovery rate threshold to define positive examples in training" help=""/>
125 <expand macro="adv_opts_macro"> 123 <expand macro="adv_opts_macro">
126 <param name="custom_enzyme" argument="-custom_enzyme" type="text" optional="true" value="" label="Specify rules for in silico digestion of protein sequences" help="Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. "> 124 <param argument="-custom_enzyme" type="text" optional="true" value="" label="Specify rules for in silico digestion of protein sequences" help="Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. ">
127 <expand macro="list_string_san"/> 125 <expand macro="list_string_san" name="custom_enzyme"/>
128 </param> 126 </param>
129 <param name="decoy_prefix" argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help=""> 127 <param argument="-decoy_prefix" type="text" optional="true" value="decoy_" label="Specifies the prefix of the protein names that indicate a decoy" help="">
130 <expand macro="list_string_san"/> 128 <expand macro="list_string_san" name="decoy_prefix"/>
131 </param> 129 </param>
132 <param name="deisotope" argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/> 130 <param argument="-deisotope" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Deisotope spectra before searching" help=""/>
133 <param name="report_decoys" argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/> 131 <param argument="-report_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include decoys in the final reported dataset" help=""/>
134 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 132 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
135 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 133 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
136 <expand macro="list_string_san"/> 134 <expand macro="list_string_san" name="test"/>
137 </param> 135 </param>
138 </expand> 136 </expand>
139 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 137 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
140 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 138 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
141 </param> 139 </param>
144 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 142 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
145 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 143 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
146 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 144 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
147 </data> 145 </data>
148 </outputs> 146 </outputs>
149 <tests> 147 <tests><!-- TOPP_CruxAdapter_1 -->
150 <expand macro="autotest_CruxAdapter"/> 148 <test expect_num_outputs="2">
151 <expand macro="manutest_CruxAdapter"/> 149 <section name="adv_opts">
150 <param name="custom_enzyme" value=""/>
151 <param name="decoy_prefix" value="decoy_"/>
152 <param name="deisotope" value="false"/>
153 <param name="report_decoys" value="false"/>
154 <param name="force" value="false"/>
155 <param name="test" value="true"/>
156 </section>
157 <param name="in" value="spectra_comet.mzML"/>
158 <output name="out" file="CruxAdapter_1_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
159 <param name="database" value="proteins.fasta"/>
160 <param name="extra_index_args" value=""/>
161 <param name="extra_search_args" value=""/>
162 <param name="extra_percolator_args" value=""/>
163 <param name="precursor_mass_tolerance" value="10.0"/>
164 <param name="precursor_mass_units" value="ppm"/>
165 <param name="fragment_bin_offset" value="0.0"/>
166 <param name="fragment_bin_width" value="0.02"/>
167 <param name="isotope_error" value=""/>
168 <param name="run_percolator" value="false"/>
169 <param name="enzyme" value="trypsin"/>
170 <param name="digestion" value="full-digest"/>
171 <param name="allowed_missed_cleavages" value="0"/>
172 <param name="decoy_format" value="peptide-reverse"/>
173 <param name="keep_terminal_aminos" value="NC"/>
174 <param name="cterm_modifications" value=""/>
175 <param name="nterm_modifications" value=""/>
176 <param name="modifications" value=""/>
177 <param name="test_fdr" value="0.01"/>
178 <param name="train_fdr" value="0.01"/>
179 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
180 <output name="ctd_out" ftype="xml">
181 <assert_contents>
182 <is_valid_xml/>
183 </assert_contents>
184 </output>
185 </test>
152 </tests> 186 </tests>
153 <help><![CDATA[Identifies MS/MS spectra using Crux. 187 <help><![CDATA[Identifies MS/MS spectra using Crux.
154 188
155 189
156 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_CruxAdapter.html]]></help> 190 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_CruxAdapter.html]]></help>
157 <expand macro="references"/> 191 <expand macro="references"/>
158 </tool> 192 </tool>