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comparison MSFraggerAdapter.xml @ 0:52a0856534d9 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:48:23 +0000
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children 5a9c3e827da5
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-1:000000000000 0:52a0856534d9
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="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Peptide Identification with MSFragger</description>
6 <macros>
7 <token name="@EXECUTABLE@">MSFraggerAdapter</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($in.ext)' &&
21 mkdir out &&
22 #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
23 mkdir opt_out &&
24 #end if
25 mkdir database &&
26 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
27
28 ## Main program call
29
30 set -o pipefail &&
31 @EXECUTABLE@ -write_ctd ./ &&
32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
34 -in
35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
36 -out
37 'out/output.${gxy2omsext("idxml")}'
38 #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
39 -opt_out
40 'opt_out/output.${gxy2omsext("pepxml")}'
41 #end if
42 -database
43 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
44 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
45 | tee '$stdout'
46 #end if
47
48 ## Postprocessing
49 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
50 #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
51 && mv 'opt_out/output.${gxy2omsext("pepxml")}' '$opt_out'
52 #end if
53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
54 && mv '@EXECUTABLE@.ctd' '$ctd_out'
55 #end if]]></command>
56 <configfiles>
57 <inputs name="args_json" data_style="paths"/>
58 <configfile name="hardcoded_json"><![CDATA[{"java_executable": "java", "executable": "/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
59 </configfiles>
60 <inputs>
61 <param name="java_heapmemory" argument="-java_heapmemory" type="integer" optional="true" value="3500" label="Maximum Java heap size (in MB)" help=""/>
62 <param name="in" argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/>
63 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="Protein FASTA database file path" help=" select fasta data sets(s)"/>
64 <section name="tolerance" title="Search Tolerances" help="" expanded="false">
65 <param name="precursor_mass_tolerance" argument="-tolerance:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Precursor mass tolerance (window is +/- this value)" help=""/>
66 <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
67 <option value="Da">Da</option>
68 <option value="ppm" selected="true">ppm</option>
69 <expand macro="list_string_san"/>
70 </param>
71 <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" optional="true" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/>
72 <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" display="radio" type="select" optional="false" label="Unit of precursor true tolerance" help="">
73 <option value="Da">Da</option>
74 <option value="ppm" selected="true">ppm</option>
75 <expand macro="list_string_san"/>
76 </param>
77 <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/>
78 <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
79 <option value="Da">Da</option>
80 <option value="ppm" selected="true">ppm</option>
81 <expand macro="list_string_san"/>
82 </param>
83 <param name="isotope_error" argument="-tolerance:isotope_error" display="radio" type="select" optional="false" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12">
84 <option value="0" selected="true">0</option>
85 <option value="1">1</option>
86 <option value="2">2</option>
87 <expand macro="list_string_san"/>
88 </param>
89 </section>
90 <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false">
91 <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="false" label="Name of the enzyme to be written to the pepXML file" help="">
92 <option value="Glu-C+P">Glu-C+P</option>
93 <option value="PepsinA + P">PepsinA + P</option>
94 <option value="cyanogen-bromide">cyanogen-bromide</option>
95 <option value="Clostripain/P">Clostripain/P</option>
96 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
97 <option value="no cleavage">no cleavage</option>
98 <option value="unspecific cleavage">unspecific cleavage</option>
99 <option value="2-iodobenzoate">2-iodobenzoate</option>
100 <option value="iodosobenzoate">iodosobenzoate</option>
101 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
102 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
103 <option value="V8-E">V8-E</option>
104 <option value="leukocyte elastase">leukocyte elastase</option>
105 <option value="Arg-C">Arg-C</option>
106 <option value="Arg-C/P">Arg-C/P</option>
107 <option value="Asp-N">Asp-N</option>
108 <option value="Asp-N/B">Asp-N/B</option>
109 <option value="Asp-N_ambic">Asp-N_ambic</option>
110 <option value="Chymotrypsin">Chymotrypsin</option>
111 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
112 <option value="CNBr">CNBr</option>
113 <option value="Formic_acid">Formic_acid</option>
114 <option value="Lys-C">Lys-C</option>
115 <option value="Lys-N">Lys-N</option>
116 <option value="Lys-C/P">Lys-C/P</option>
117 <option value="PepsinA">PepsinA</option>
118 <option value="TrypChymo">TrypChymo</option>
119 <option value="Trypsin/P">Trypsin/P</option>
120 <option value="V8-DE">V8-DE</option>
121 <option value="proline endopeptidase">proline endopeptidase</option>
122 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
123 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
124 <option value="Trypsin" selected="true">Trypsin</option>
125 <expand macro="list_string_san"/>
126 </param>
127 <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" optional="true" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help="">
128 <expand macro="list_string_san"/>
129 </param>
130 <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" optional="true" value="P" label="Residues that the enzyme will not cut before" help="">
131 <expand macro="list_string_san"/>
132 </param>
133 <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" display="radio" type="select" optional="false" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help="">
134 <option value="non-enzymatic">non-enzymatic</option>
135 <option value="semi">semi</option>
136 <option value="fully" selected="true">fully</option>
137 <expand macro="list_string_san"/>
138 </param>
139 <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" optional="false" label="Allowed number of missed cleavages" help="">
140 <option value="0">0</option>
141 <option value="1">1</option>
142 <option value="2" selected="true">2</option>
143 <option value="3">3</option>
144 <option value="4">4</option>
145 <option value="5">5</option>
146 <expand macro="list_string_san"/>
147 </param>
148 <param name="min_length" argument="-digest:min_length" type="integer" optional="true" min="0" value="7" label="Minimum length of peptides to be generated during in-silico digestion" help=""/>
149 <param name="max_length" argument="-digest:max_length" type="integer" optional="true" min="0" value="64" label="Maximum length of peptides to be generated during in-silico digestion" help=""/>
150 <param name="mass_range_min" argument="-digest:mass_range_min" type="float" optional="true" min="0.0" value="500.0" label="Min mass of peptides to be generated (Da)" help=""/>
151 <param name="mass_range_max" argument="-digest:mass_range_max" type="float" optional="true" min="0.0" value="5000.0" label="Max mass of peptides to be generated (Da)" help=""/>
152 </section>
153 <section name="varmod" title="Variable Modification Parameters" help="" expanded="false">
154 <param name="clip_nterm_m" argument="-varmod:clip_nterm_m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Specifies the trimming of a protein N-terminal methionine as a variable modification" help=""/>
155 <param name="masses" argument="-varmod:masses" type="text" optional="true" value="" label="Masses for variable modifications" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
156 <expand macro="list_float_valsan"/>
157 </param>
158 <param name="syntaxes" argument="-varmod:syntaxes" type="text" optional="true" value="" label="Syntax Strings for variable modifications" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
159 <expand macro="list_string_val"/>
160 <expand macro="list_string_san"/>
161 </param>
162 <param name="enable_common" argument="-varmod:enable_common" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable common variable modifications (15.9949 M and 42.0106 [^)" help=""/>
163 <param name="not_allow_multiple_variable_mods_on_residue" argument="-varmod:not_allow_multiple_variable_mods_on_residue" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not allow any one amino acid to be modified by multiple variable modifications" help=""/>
164 <param name="max_variable_mods_per_mod" argument="-varmod:max_variable_mods_per_mod" type="select" optional="false" label="Maximum number of residues that can be occupied by each variable modification" help="">
165 <option value="0">0</option>
166 <option value="1">1</option>
167 <option value="2" selected="true">2</option>
168 <option value="3">3</option>
169 <option value="4">4</option>
170 <option value="5">5</option>
171 <expand macro="list_string_san"/>
172 </param>
173 <param name="max_variable_mods_combinations" argument="-varmod:max_variable_mods_combinations" type="integer" optional="true" min="0" max="65534" value="5000" label="Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534)" help="If a greater number than the maximum is generated, only the unmodified peptide is considered"/>
174 </section>
175 <section name="spectrum" title="Spectrum Processing Parameters" help="" expanded="false">
176 <param name="minimum_peaks" argument="-spectrum:minimum_peaks" type="integer" optional="true" min="0" value="10" label="Minimum number of peaks in experimental spectrum for matching" help=""/>
177 <param name="use_topn_peaks" argument="-spectrum:use_topn_peaks" type="integer" optional="true" min="0" value="50" label="Pre-process experimental spectrum to only use top N peaks" help=""/>
178 <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/>
179 <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
180 <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
181 <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" display="radio" type="select" optional="false" label="Maximum charge state for theoretical fragments to match" help="">
182 <option value="1">1</option>
183 <option value="2" selected="true">2</option>
184 <option value="3">3</option>
185 <option value="4">4</option>
186 <expand macro="list_string_san"/>
187 </param>
188 <param name="override_charge" argument="-spectrum:override_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)" help=""/>
189 <param name="precursor_charge_min" argument="-spectrum:precursor_charge_min" type="integer" optional="true" min="0" value="1" label="Min charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
190 <param name="precursor_charge_max" argument="-spectrum:precursor_charge_max" type="integer" optional="true" min="0" value="4" label="Max charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
191 </section>
192 <section name="search" title="Open Search Features" help="" expanded="false">
193 <param name="track_zero_topn" argument="-search:track_zero_topn" type="integer" optional="true" min="0" value="0" label="Track top N unmodified peptide results separately from main results internally for boosting features" help="Should be set to a number greater than search:output_report_topN if zero bin boosting is desired"/>
194 <param name="zero_bin_accept_expect" argument="-search:zero_bin_accept_expect" type="float" optional="true" min="0.0" value="0.0" label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value" help=""/>
195 <param name="zero_bin_mult_expect" argument="-search:zero_bin_mult_expect" type="float" optional="true" min="0.0" value="1.0" label="Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)" help=""/>
196 <param name="add_topn_complementary" argument="-search:add_topn_complementary" type="integer" optional="true" min="0" value="0" label="Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum" help="Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option"/>
197 <param name="min_fragments_modeling" argument="-search:min_fragments_modeling" type="integer" optional="true" min="0" value="3" label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" help=""/>
198 <param name="min_matched_fragments" argument="-search:min_matched_fragments" type="integer" optional="true" min="0" value="4" label="Minimum number of matched peaks for PSM to be reported" help="MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches"/>
199 <param name="output_report_topn" argument="-search:output_report_topn" type="integer" optional="true" min="0" value="1" label="Reports top N PSMs per input spectrum" help=""/>
200 <param name="output_max_expect" argument="-search:output_max_expect" type="float" optional="true" min="0.0" value="50.0" label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" help=""/>
201 </section>
202 <section name="statmod" title="Static Modification Parameters" help="" expanded="false">
203 <param name="add_cterm_peptide" argument="-statmod:add_cterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of peptide" help=""/>
204 <param name="add_nterm_peptide" argument="-statmod:add_nterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of peptide" help=""/>
205 <param name="add_cterm_protein" argument="-statmod:add_cterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of protein" help=""/>
206 <param name="add_nterm_protein" argument="-statmod:add_nterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of protein" help=""/>
207 <param name="add_G_glycine" argument="-statmod:add_G_glycine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glycine" help=""/>
208 <param name="add_A_alanine" argument="-statmod:add_A_alanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to alanine" help=""/>
209 <param name="add_S_serine" argument="-statmod:add_S_serine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to serine" help=""/>
210 <param name="add_P_proline" argument="-statmod:add_P_proline" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to proline" help=""/>
211 <param name="add_V_valine" argument="-statmod:add_V_valine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to valine" help=""/>
212 <param name="add_T_threonine" argument="-statmod:add_T_threonine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to threonine" help=""/>
213 <param name="add_C_cysteine" argument="-statmod:add_C_cysteine" type="float" optional="true" min="0.0" value="57.021464" label="Statically add mass to cysteine" help=""/>
214 <param name="add_L_leucine" argument="-statmod:add_L_leucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to leucine" help=""/>
215 <param name="add_I_isoleucine" argument="-statmod:add_I_isoleucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to isoleucine" help=""/>
216 <param name="add_N_asparagine" argument="-statmod:add_N_asparagine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to asparagine" help=""/>
217 <param name="add_D_aspartic_acid" argument="-statmod:add_D_aspartic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to aspartic_acid" help=""/>
218 <param name="add_Q_glutamine" argument="-statmod:add_Q_glutamine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamine" help=""/>
219 <param name="add_K_lysine" argument="-statmod:add_K_lysine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to lysine" help=""/>
220 <param name="add_E_glutamic_acid" argument="-statmod:add_E_glutamic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamic_acid" help=""/>
221 <param name="add_M_methionine" argument="-statmod:add_M_methionine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to methionine" help=""/>
222 <param name="add_H_histidine" argument="-statmod:add_H_histidine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to histidine" help=""/>
223 <param name="add_F_phenylalanine" argument="-statmod:add_F_phenylalanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to phenylalanine" help=""/>
224 <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/>
225 <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/>
226 <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/>
227 </section>
228 <expand macro="adv_opts_macro">
229 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
230 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
231 <expand macro="list_string_san"/>
232 </param>
233 </expand>
234 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
235 <option value="opt_out_FLAG">opt_out (Statically add mass to tryptophan)</option>
236 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
237 </param>
238 </inputs>
239 <outputs>
240 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
241 <data name="opt_out" label="${tool.name} on ${on_string}: opt_out" format="pepxml">
242 <filter>OPTIONAL_OUTPUTS is not None and "opt_out_FLAG" in OPTIONAL_OUTPUTS</filter>
243 </data>
244 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
245 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
246 </data>
247 </outputs>
248 <tests>
249 <expand macro="autotest_MSFraggerAdapter"/>
250 <expand macro="manutest_MSFraggerAdapter"/>
251 </tests>
252 <help><![CDATA[Peptide Identification with MSFragger
253
254
255 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/TOPP_MSFraggerAdapter.html]]></help>
256 <expand macro="references"/>
257 </tool>