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comparison NucleicAcidSearchEngine.xml @ 4:92864c71ac6a draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:13:13 +0000
parents 00b91aaec050
children
comparison
equal deleted inserted replaced
3:55290cddb679 4:92864c71ac6a
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="NucleicAcidSearchEngine" name="NucleicAcidSearchEngine" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="NucleicAcidSearchEngine" name="NucleicAcidSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Annotate nucleic acid identifications to MS/MS spectra.</description> 5 <description>Annotate nucleic acid identifications to MS/MS spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">NucleicAcidSearchEngine</token> 7 <token name="@EXECUTABLE@">NucleicAcidSearchEngine</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@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in && 17 mkdir in &&
20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
21 mkdir database && 19 #if $database:
22 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && 20 mkdir database &&
21 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
22 #end if
23 #if $digest:
24 mkdir digest &&
25 ln -s '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' &&
26 #end if
23 mkdir out && 27 mkdir out &&
24 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 28 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir id_out && 29 mkdir id_out &&
30 #end if
31 #if "db_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
32 mkdir db_out &&
33 #end if
34 #if "digest_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
35 mkdir digest_out &&
26 #end if 36 #end if
27 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 37 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir lfq_out && 38 mkdir lfq_out &&
29 #end if 39 #end if
30 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 40 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
40 @EXECUTABLE@ -write_ctd ./ && 50 @EXECUTABLE@ -write_ctd ./ &&
41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 51 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 52 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
43 -in 53 -in
44 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' 54 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
45 -database 55 #if $database:
46 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' 56 -database
57 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
58 #end if
59 #if $digest:
60 -digest
61 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)'
62 #end if
47 -out 63 -out
48 'out/output.${gxy2omsext("mztab")}' 64 'out/output.${gxy2omsext("mztab")}'
49 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 65 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
50 -id_out 66 -id_out
51 'id_out/output.${gxy2omsext("idxml")}' 67 'id_out/output.${gxy2omsext("idxml")}'
52 #end if 68 #end if
69 #if "db_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
70 -db_out
71 'db_out/output.${gxy2omsext("sqlite")}'
72 #end if
73 #if "digest_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
74 -digest_out
75 'digest_out/output.${gxy2omsext("sqlite")}'
76 #end if
53 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 77 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
54 -lfq_out 78 -lfq_out
55 'lfq_out/output.${gxy2omsext("tabular")}' 79 'lfq_out/output.${gxy2omsext("tabular")}'
56 #end if 80 #end if
57 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 81 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
68 92
69 ## Postprocessing 93 ## Postprocessing
70 && mv 'out/output.${gxy2omsext("mztab")}' '$out' 94 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
71 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 95 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
72 && mv 'id_out/output.${gxy2omsext("idxml")}' '$id_out' 96 && mv 'id_out/output.${gxy2omsext("idxml")}' '$id_out'
97 #end if
98 #if "db_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
99 && mv 'db_out/output.${gxy2omsext("sqlite")}' '$db_out'
100 #end if
101 #if "digest_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
102 && mv 'digest_out/output.${gxy2omsext("sqlite")}' '$digest_out'
73 #end if 103 #end if
74 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 104 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
75 && mv 'lfq_out/output.${gxy2omsext("tabular")}' '$lfq_out' 105 && mv 'lfq_out/output.${gxy2omsext("tabular")}' '$lfq_out'
76 #end if 106 #end if
77 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 107 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
86 <configfiles> 116 <configfiles>
87 <inputs name="args_json" data_style="paths"/> 117 <inputs name="args_json" data_style="paths"/>
88 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 118 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
89 </configfiles> 119 </configfiles>
90 <inputs> 120 <inputs>
91 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file: spectra" help=" select mzml data sets(s)"/> 121 <param argument="-in" type="data" format="mzml" optional="false" label="Input file: spectra" help=" select mzml data sets(s)"/>
92 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="Input file: sequence database" help=" select fasta data sets(s)"/> 122 <param argument="-database" type="data" format="fasta" optional="true" label="Input file: sequence database" help="Required unless 'digest' is set select fasta data sets(s)"/>
93 <section name="precursor" title="Precursor (Parent Ion) Options" help="" expanded="false"> 123 <param argument="-digest" type="data" format="sqlite" optional="true" label="Input file: pre-digested sequence database" help="Can be used instead of 'database'. Sets all 'oligo:...' parameters select sqlite data sets(s)"/>
124 <section name="precursor" title="Precursor (parent ion) options" help="" expanded="false">
94 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/> 125 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" optional="true" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/>
95 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help=""> 126 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help="">
96 <option value="Da">Da</option> 127 <option value="Da">Da</option>
97 <option value="ppm" selected="true">ppm</option> 128 <option value="ppm" selected="true">ppm</option>
98 <expand macro="list_string_san"/> 129 <expand macro="list_string_san" name="mass_tolerance_unit"/>
99 </param> 130 </param>
100 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="-1" label="Minimum precursor charge to be considered" help=""/> 131 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="-1" label="Minimum precursor charge to be considered" help=""/>
101 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="-20" label="Maximum precursor charge to be considered" help=""/> 132 <param name="max_charge" argument="-precursor:max_charge" type="integer" optional="true" value="-20" label="Maximum precursor charge to be considered" help=""/>
102 <param name="include_unknown_charge" argument="-precursor:include_unknown_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include MS2 spectra with unknown precursor charge - try to match them in any possible charge between 'min_charge' and 'max_charge', at the risk of a higher error rate" help=""/> 133 <param name="include_unknown_charge" argument="-precursor:include_unknown_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Include MS2 spectra with unknown precursor charge - try to match them in any possible charge between 'min_charge' and 'max_charge', at the risk of a higher error rate" help=""/>
103 <param name="use_avg_mass" argument="-precursor:use_avg_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use average instead of monoisotopic precursor masses (appropriate for low-resolution instruments)" help=""/> 134 <param name="use_avg_mass" argument="-precursor:use_avg_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use average instead of monoisotopic precursor masses (appropriate for low-resolution instruments)" help=""/>
104 <param name="use_adducts" argument="-precursor:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider possible salt adducts (see 'precursor:potential_adducts') when matching precursor masses" help=""/> 135 <param name="use_adducts" argument="-precursor:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consider possible salt adducts (see 'precursor:potential_adducts') when matching precursor masses" help=""/>
105 <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" optional="true" value="Na:+" label="Adducts considered to explain mass differences" help="Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 136 <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" optional="true" value="Na:+" label="Adducts considered to explain mass differences" help="Format: 'Element:Charge(+/-)', i.e. the number of '+' or '-' indicates the charge, e.g. 'Ca:++' indicates +2. Only used if 'precursor:use_adducts' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
106 <expand macro="list_string_val"/> 137 <expand macro="list_string_val" name="potential_adducts"/>
107 <expand macro="list_string_san"/> 138 <expand macro="list_string_san" name="potential_adducts"/>
108 </param> 139 </param>
109 <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1 2 3 4" label="Correct for mono-isotopic peak misassignments" help="E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 140 <param name="isotopes" argument="-precursor:isotopes" type="text" optional="true" value="0 1 2 3 4" label="Correct for mono-isotopic peak misassignments" help="E.g.: 1 = precursor may be misassigned to the first isotopic peak. Ignored if 'use_avg_mass' is set (space separated list, in order to allow for spaces in list items surround them by single quotes)">
110 <expand macro="list_integer_valsan"/> 141 <expand macro="list_integer_valsan" name="isotopes"/>
111 </param> 142 </param>
112 </section> 143 </section>
113 <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false"> 144 <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false">
114 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/> 145 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" optional="true" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
115 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help=""> 146 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
116 <option value="Da">Da</option> 147 <option value="Da">Da</option>
117 <option value="ppm" selected="true">ppm</option> 148 <option value="ppm" selected="true">ppm</option>
118 <expand macro="list_string_san"/> 149 <expand macro="list_string_san" name="mass_tolerance_unit"/>
119 </param> 150 </param>
120 <param name="ions" argument="-fragment:ions" multiple="true" type="select" optional="true" label="Fragment ions to include in theoretical spectra" help=""> 151 <param name="ions" argument="-fragment:ions" multiple="true" type="select" optional="true" label="Fragment ions to include in theoretical spectra" help="">
121 <option value="a-B" selected="true">a-B</option> 152 <option value="a-B" selected="true">a-B</option>
122 <option value="a" selected="true">a</option> 153 <option value="a" selected="true">a</option>
123 <option value="b" selected="true">b</option> 154 <option value="b" selected="true">b</option>
125 <option value="d" selected="true">d</option> 156 <option value="d" selected="true">d</option>
126 <option value="w" selected="true">w</option> 157 <option value="w" selected="true">w</option>
127 <option value="x" selected="true">x</option> 158 <option value="x" selected="true">x</option>
128 <option value="y" selected="true">y</option> 159 <option value="y" selected="true">y</option>
129 <option value="z" selected="true">z</option> 160 <option value="z" selected="true">z</option>
130 <expand macro="list_string_san"/> 161 <expand macro="list_string_san" name="ions"/>
131 </param> 162 </param>
132 </section> 163 </section>
133 <section name="modifications" title="Modifications Options" help="" expanded="false"> 164 <section name="modifications" title="Modification options" help="" expanded="false">
134 <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications" help=""> 165 <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications" help="">
135 <option value="">default (nothing chosen)</option>
136 <option value="m1Am">m1Am</option> 166 <option value="m1Am">m1Am</option>
137 <option value="m1Gm">m1Gm</option> 167 <option value="m1Gm">m1Gm</option>
138 <option value="m1Im">m1Im</option> 168 <option value="m1Im">m1Im</option>
139 <option value="m1acp3Y">m1acp3Y</option> 169 <option value="m1acp3Y">m1acp3Y</option>
140 <option value="m1A">m1A</option> 170 <option value="m1A">m1A</option>
299 <option value="N">N</option> 329 <option value="N">N</option>
300 <option value="cmo5U">cmo5U</option> 330 <option value="cmo5U">cmo5U</option>
301 <option value="mcmo5U">mcmo5U</option> 331 <option value="mcmo5U">mcmo5U</option>
302 <option value="yW">yW</option> 332 <option value="yW">yW</option>
303 <option value="imG">imG</option> 333 <option value="imG">imG</option>
334 <option value="dA">dA</option>
335 <option value="dC">dC</option>
336 <option value="dG">dG</option>
337 <option value="dU">dU</option>
338 <option value="dT">dT</option>
304 <option value="3'-p">3'-p</option> 339 <option value="3'-p">3'-p</option>
305 <option value="5'-p">5'-p</option> 340 <option value="5'-p">5'-p</option>
306 <option value="mA">mA</option> 341 <option value="mA">mA</option>
307 <option value="mC">mC</option> 342 <option value="mC">mC</option>
308 <option value="mG">mG</option> 343 <option value="mG">mG</option>
328 <option value="mmC?">mmC?</option> 363 <option value="mmC?">mmC?</option>
329 <option value="mmG?">mmG?</option> 364 <option value="mmG?">mmG?</option>
330 <option value="mmmG?">mmmG?</option> 365 <option value="mmmG?">mmmG?</option>
331 <option value="ac4C/f5Cm?">ac4C/f5Cm?</option> 366 <option value="ac4C/f5Cm?">ac4C/f5Cm?</option>
332 <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option> 367 <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option>
333 <expand macro="list_string_san"/> 368 <expand macro="list_string_san" name="variable"/>
334 </param> 369 </param>
335 <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/> 370 <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" optional="true" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/>
336 <param name="resolve_ambiguities" argument="-modifications:resolve_ambiguities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Attempt to resolve ambiguous modifications" help="(e.g. 'mA?' for 'mA'/'Am') based on a-B ions.. This incurs a performance cost because two modifications have to be considered for each case.. Requires a-B ions to be enabled in parameter 'fragment:ions'"/> 371 <param name="resolve_ambiguities" argument="-modifications:resolve_ambiguities" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Attempt to resolve ambiguous modifications" help="(e.g. 'mA?' for 'mA'/'Am') based on a-B ions.. This incurs a performance cost because two modifications have to be considered for each case.. Requires a-B ions to be enabled in parameter 'fragment:ions'"/>
337 </section> 372 </section>
338 <section name="oligo" title="Oligonucleotide Options" help="" expanded="false"> 373 <section name="oligo" title="Oligonucleotide (digestion) options (ignored if 'digest' input is used)" help="" expanded="false">
339 <param name="min_size" argument="-oligo:min_size" type="integer" optional="true" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" help=""/> 374 <param name="min_size" argument="-oligo:min_size" type="integer" optional="true" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" help=""/>
340 <param name="max_size" argument="-oligo:max_size" type="integer" optional="true" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/> 375 <param name="max_size" argument="-oligo:max_size" type="integer" optional="true" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/>
341 <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> 376 <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/>
342 <param name="enzyme" argument="-oligo:enzyme" type="select" optional="false" label="The enzyme used for RNA digestion" help=""> 377 <param name="enzyme" argument="-oligo:enzyme" type="select" optional="true" label="The enzyme used for RNA digestion" help="">
343 <option value="RNase_T1">RNase_T1</option> 378 <option value="RNase_T1">RNase_T1</option>
344 <option value="cusativin">cusativin</option> 379 <option value="cusativin">cusativin</option>
380 <option value="RNase_H">RNase_H</option>
381 <option value="mazF">mazF</option>
382 <option value="colicin_E5">colicin_E5</option>
383 <option value="no cleavage" selected="true">no cleavage</option>
345 <option value="RNase_U2">RNase_U2</option> 384 <option value="RNase_U2">RNase_U2</option>
346 <option value="RNase_A">RNase_A</option> 385 <option value="RNase_A">RNase_A</option>
347 <option value="RNase_MC1">RNase_MC1</option> 386 <option value="RNase_MC1">RNase_MC1</option>
348 <option value="RNase_H">RNase_H</option>
349 <option value="no cleavage" selected="true">no cleavage</option>
350 <option value="unspecific cleavage">unspecific cleavage</option> 387 <option value="unspecific cleavage">unspecific cleavage</option>
351 <expand macro="list_string_san"/> 388 <expand macro="list_string_san" name="enzyme"/>
352 </param> 389 </param>
353 </section> 390 </section>
354 <section name="report" title="Reporting Options" help="" expanded="false"> 391 <section name="report" title="Reporting Options" help="" expanded="false">
355 <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/> 392 <param name="top_hits" argument="-report:top_hits" type="integer" optional="true" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/>
356 </section> 393 </section>
357 <section name="fdr" title="False Discovery Rate Options" help="" expanded="false"> 394 <section name="fdr" title="False Discovery Rate options" help="" expanded="false">
358 <param name="decoy_pattern" argument="-fdr:decoy_pattern" type="text" optional="true" value="" label="String used as part of the accession to annotate decoy sequences" help="(e.g. 'DECOY_'). Leave empty to skip the FDR/q-value calculation"> 395 <param name="decoy_pattern" argument="-fdr:decoy_pattern" type="text" optional="true" value="" label="String used as part of the accession to annotate decoy sequences" help="(e.g. 'DECOY_'). Leave empty to skip the FDR/q-value calculation">
359 <expand macro="list_string_san"/> 396 <expand macro="list_string_san" name="decoy_pattern"/>
360 </param> 397 </param>
361 <param name="cutoff" argument="-fdr:cutoff" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/> 398 <param name="cutoff" argument="-fdr:cutoff" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Cut-off for FDR filtering; search hits with higher q-values will be removed" help=""/>
362 <param name="remove_decoys" argument="-fdr:remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not score hits to decoy sequences and remove them when filtering" help=""/> 399 <param name="remove_decoys" argument="-fdr:remove_decoys" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not score hits to decoy sequences and remove them when filtering" help=""/>
363 </section> 400 </section>
364 <expand macro="adv_opts_macro"> 401 <expand macro="adv_opts_macro">
365 <param name="decharge_ms2" argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/> 402 <param argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/>
366 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 403 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
367 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 404 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
368 <expand macro="list_string_san"/> 405 <expand macro="list_string_san" name="test"/>
369 </param> 406 </param>
370 </expand> 407 </expand>
371 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 408 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
372 <option value="id_out_FLAG">id_out (Output file: idXML (for visualization in TOPPView))</option> 409 <option value="id_out_FLAG">id_out (Output file: idXML (for visualization in TOPPView))</option>
373 <option value="lfq_out_FLAG">lfq_out (Output file: Targets for label-free quantification using FeatureFinderMetaboIdent ('id' input))</option> 410 <option value="db_out_FLAG">db_out (Output file: oms (SQLite database))</option>
411 <option value="digest_out_FLAG">digest_out (Output file: sequence database digest)</option>
412 <option value="lfq_out_FLAG">lfq_out (Output file: targets for label-free quantification using FeatureFinderMetaboIdent ('id' input))</option>
374 <option value="theo_ms2_out_FLAG">theo_ms2_out (Output file: theoretical MS2 spectra for precursor mass matches)</option> 413 <option value="theo_ms2_out_FLAG">theo_ms2_out (Output file: theoretical MS2 spectra for precursor mass matches)</option>
375 <option value="exp_ms2_out_FLAG">exp_ms2_out (Output file: experimental MS2 spectra for precursor mass matches)</option> 414 <option value="exp_ms2_out_FLAG">exp_ms2_out (Output file: experimental MS2 spectra for precursor mass matches)</option>
376 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 415 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
377 </param> 416 </param>
378 </inputs> 417 </inputs>
379 <outputs> 418 <outputs>
380 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/> 419 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
381 <data name="id_out" label="${tool.name} on ${on_string}: id_out" format="idxml"> 420 <data name="id_out" label="${tool.name} on ${on_string}: id_out" format="idxml">
382 <filter>OPTIONAL_OUTPUTS is not None and "id_out_FLAG" in OPTIONAL_OUTPUTS</filter> 421 <filter>OPTIONAL_OUTPUTS is not None and "id_out_FLAG" in OPTIONAL_OUTPUTS</filter>
383 </data> 422 </data>
423 <data name="db_out" label="${tool.name} on ${on_string}: db_out" format="sqlite">
424 <filter>OPTIONAL_OUTPUTS is not None and "db_out_FLAG" in OPTIONAL_OUTPUTS</filter>
425 </data>
426 <data name="digest_out" label="${tool.name} on ${on_string}: digest_out" format="sqlite">
427 <filter>OPTIONAL_OUTPUTS is not None and "digest_out_FLAG" in OPTIONAL_OUTPUTS</filter>
428 </data>
384 <data name="lfq_out" label="${tool.name} on ${on_string}: lfq_out" format="tabular"> 429 <data name="lfq_out" label="${tool.name} on ${on_string}: lfq_out" format="tabular">
385 <filter>OPTIONAL_OUTPUTS is not None and "lfq_out_FLAG" in OPTIONAL_OUTPUTS</filter> 430 <filter>OPTIONAL_OUTPUTS is not None and "lfq_out_FLAG" in OPTIONAL_OUTPUTS</filter>
386 </data> 431 </data>
387 <data name="theo_ms2_out" label="${tool.name} on ${on_string}: theo_ms2_out" format="mzml"> 432 <data name="theo_ms2_out" label="${tool.name} on ${on_string}: theo_ms2_out" format="mzml">
388 <filter>OPTIONAL_OUTPUTS is not None and "theo_ms2_out_FLAG" in OPTIONAL_OUTPUTS</filter> 433 <filter>OPTIONAL_OUTPUTS is not None and "theo_ms2_out_FLAG" in OPTIONAL_OUTPUTS</filter>
392 </data> 437 </data>
393 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 438 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
394 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 439 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
395 </data> 440 </data>
396 </outputs> 441 </outputs>
397 <tests> 442 <tests><!-- UTILS_NucleicAcidSearchEngine_1 -->
398 <expand macro="autotest_NucleicAcidSearchEngine"/> 443 <test expect_num_outputs="5">
399 <expand macro="manutest_NucleicAcidSearchEngine"/> 444 <section name="adv_opts">
445 <param name="decharge_ms2" value="false"/>
446 <param name="force" value="false"/>
447 <param name="test" value="true"/>
448 </section>
449 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
450 <param name="database" value="NucleicAcidSearchEngine_1.fasta"/>
451 <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
452 <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
453 <output name="db_out" file="NucleicAcidSearchEngine_13_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
454 <output name="digest_out" file="NucleicAcidSearchEngine_1_digest.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
455 <section name="precursor">
456 <param name="mass_tolerance" value="5.0"/>
457 <param name="mass_tolerance_unit" value="ppm"/>
458 <param name="min_charge" value="-2"/>
459 <param name="max_charge" value="-14"/>
460 <param name="include_unknown_charge" value="true"/>
461 <param name="use_avg_mass" value="false"/>
462 <param name="use_adducts" value="false"/>
463 <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
464 <param name="isotopes" value="0 1 2"/>
465 </section>
466 <section name="fragment">
467 <param name="mass_tolerance" value="5.0"/>
468 <param name="mass_tolerance_unit" value="ppm"/>
469 <param name="ions" value="a-B,c,w,y"/>
470 </section>
471 <section name="modifications">
472 <param name="variable"/>
473 <param name="variable_max_per_oligo" value="2"/>
474 <param name="resolve_ambiguities" value="false"/>
475 </section>
476 <section name="oligo">
477 <param name="min_size" value="5"/>
478 <param name="max_size" value="0"/>
479 <param name="missed_cleavages" value="22"/>
480 <param name="enzyme" value="no cleavage"/>
481 </section>
482 <section name="report">
483 <param name="top_hits" value="1"/>
484 </section>
485 <section name="fdr">
486 <param name="decoy_pattern" value="DECOY_"/>
487 <param name="cutoff" value="0.05"/>
488 <param name="remove_decoys" value="true"/>
489 </section>
490 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG,db_out_FLAG,digest_out_FLAG"/>
491 <output name="ctd_out" ftype="xml">
492 <assert_contents>
493 <is_valid_xml/>
494 </assert_contents>
495 </output>
496 </test>
497 <!-- UTILS_NucleicAcidSearchEngine_2 -->
498 <test expect_num_outputs="4">
499 <section name="adv_opts">
500 <param name="decharge_ms2" value="false"/>
501 <param name="force" value="false"/>
502 <param name="test" value="true"/>
503 </section>
504 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
505 <param name="digest" value="NucleicAcidSearchEngine_1_digest.oms"/>
506 <output name="out" file="NucleicAcidSearchEngine_12_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
507 <output name="id_out" file="NucleicAcidSearchEngine_11_out.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
508 <output name="db_out" file="NucleicAcidSearchEngine_23_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
509 <section name="precursor">
510 <param name="mass_tolerance" value="5.0"/>
511 <param name="mass_tolerance_unit" value="ppm"/>
512 <param name="min_charge" value="-2"/>
513 <param name="max_charge" value="-14"/>
514 <param name="include_unknown_charge" value="true"/>
515 <param name="use_avg_mass" value="false"/>
516 <param name="use_adducts" value="false"/>
517 <param name="potential_adducts" value="&quot;K:+&quot; &quot;Na:+&quot; &quot;Na2:++&quot; &quot;K2:++&quot; &quot;NaK:++&quot; &quot;K3:+++&quot; &quot;Na3:+++&quot; &quot;NaK2:+++&quot; &quot;Na2K:+++&quot;"/>
518 <param name="isotopes" value="0 1 2"/>
519 </section>
520 <section name="fragment">
521 <param name="mass_tolerance" value="5.0"/>
522 <param name="mass_tolerance_unit" value="ppm"/>
523 <param name="ions" value="a-B,c,w,y"/>
524 </section>
525 <section name="modifications">
526 <param name="variable"/>
527 <param name="variable_max_per_oligo" value="2"/>
528 <param name="resolve_ambiguities" value="false"/>
529 </section>
530 <section name="oligo">
531 <param name="min_size" value="5"/>
532 <param name="max_size" value="0"/>
533 <param name="missed_cleavages" value="22"/>
534 <param name="enzyme" value="no cleavage"/>
535 </section>
536 <section name="report">
537 <param name="top_hits" value="1"/>
538 </section>
539 <section name="fdr">
540 <param name="decoy_pattern" value="DECOY_"/>
541 <param name="cutoff" value="0.05"/>
542 <param name="remove_decoys" value="true"/>
543 </section>
544 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,id_out_FLAG,db_out_FLAG"/>
545 <output name="ctd_out" ftype="xml">
546 <assert_contents>
547 <is_valid_xml/>
548 </assert_contents>
549 </output>
550 </test>
400 </tests> 551 </tests>
401 <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra. 552 <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra.
402 553
403 554
404 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_NucleicAcidSearchEngine.html]]></help> 555 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NucleicAcidSearchEngine.html]]></help>
405 <expand macro="references"/> 556 <expand macro="references"/>
406 </tool> 557 </tool>