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comparison NucleicAcidSearchEngine.xml @ 5:a19e844b82ad draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:31:16 +0000
parents 92864c71ac6a
children
comparison
equal deleted inserted replaced
4:92864c71ac6a 5:a19e844b82ad
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: [RNA]-->
4 <tool id="NucleicAcidSearchEngine" name="NucleicAcidSearchEngine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Annotate nucleic acid identifications to MS/MS spectra</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">NucleicAcidSearchEngine</token> 6 <token name="@EXECUTABLE@">NucleicAcidSearchEngine</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 #if $database: 18 #if $database:
20 mkdir database && 19 mkdir database &&
21 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' && 20 cp '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
22 #end if 21 #end if
23 #if $digest: 22 #if $digest:
24 mkdir digest && 23 mkdir digest &&
25 ln -s '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' && 24 cp '$digest' 'digest/${re.sub("[^\w\-_]", "_", $digest.element_identifier)}.$gxy2omsext($digest.ext)' &&
26 #end if 25 #end if
27 mkdir out && 26 mkdir out &&
28 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 27 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
29 mkdir id_out && 28 mkdir id_out &&
30 #end if 29 #end if
116 <configfiles> 115 <configfiles>
117 <inputs name="args_json" data_style="paths"/> 116 <inputs name="args_json" data_style="paths"/>
118 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 117 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
119 </configfiles> 118 </configfiles>
120 <inputs> 119 <inputs>
121 <param argument="-in" type="data" format="mzml" optional="false" label="Input file: spectra" help=" select mzml data sets(s)"/> 120 <param argument="-in" type="data" format="mzml" label="Input file: spectra" help=" select mzml 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)"/> 121 <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)"/>
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)"/> 122 <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"> 123 <section name="precursor" title="Precursor (parent ion) options" help="" expanded="false">
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=""/> 124 <param name="mass_tolerance" argument="-precursor:mass_tolerance" type="float" value="10.0" label="Precursor mass tolerance (+/- around uncharged precursor mass)" help=""/>
126 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" optional="true" label="Unit of precursor mass tolerance" help=""> 125 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" type="select" label="Unit of precursor mass tolerance" help="">
127 <option value="Da">Da</option> 126 <option value="Da">Da</option>
128 <option value="ppm" selected="true">ppm</option> 127 <option value="ppm" selected="true">ppm</option>
129 <expand macro="list_string_san" name="mass_tolerance_unit"/> 128 <expand macro="list_string_san" name="mass_tolerance_unit"/>
130 </param> 129 </param>
131 <param name="min_charge" argument="-precursor:min_charge" type="integer" optional="true" value="-1" label="Minimum precursor charge to be considered" help=""/> 130 <param name="min_charge" argument="-precursor:min_charge" type="integer" value="-1" label="Minimum 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=""/> 131 <param name="max_charge" argument="-precursor:max_charge" type="integer" value="-20" label="Maximum precursor charge to be considered" 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=""/> 132 <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=""/>
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=""/> 133 <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=""/>
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=""/> 134 <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=""/>
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)"> 135 <param name="potential_adducts" argument="-precursor:potential_adducts" type="text" 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)">
137 <expand macro="list_string_val" name="potential_adducts"/> 136 <expand macro="list_string_val" name="potential_adducts"/>
138 <expand macro="list_string_san" name="potential_adducts"/> 137 <expand macro="list_string_san" name="potential_adducts"/>
139 </param> 138 </param>
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)"> 139 <param name="isotopes" argument="-precursor:isotopes" type="text" 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)">
141 <expand macro="list_integer_valsan" name="isotopes"/> 140 <expand macro="list_integer_valsan" name="isotopes"/>
142 </param> 141 </param>
143 </section> 142 </section>
144 <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false"> 143 <section name="fragment" title="Fragment (Product Ion) Options" help="" expanded="false">
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=""/> 144 <param name="mass_tolerance" argument="-fragment:mass_tolerance" type="float" value="10.0" label="Fragment mass tolerance (+/- around fragment m/z)" help=""/>
146 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help=""> 145 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" type="select" label="Unit of fragment mass tolerance" help="">
147 <option value="Da">Da</option> 146 <option value="Da">Da</option>
148 <option value="ppm" selected="true">ppm</option> 147 <option value="ppm" selected="true">ppm</option>
149 <expand macro="list_string_san" name="mass_tolerance_unit"/> 148 <expand macro="list_string_san" name="mass_tolerance_unit"/>
150 </param> 149 </param>
151 <param name="ions" argument="-fragment:ions" multiple="true" type="select" optional="true" label="Fragment ions to include in theoretical spectra" help=""> 150 <param name="ions" argument="-fragment:ions" type="select" multiple="true" optional="false" label="Fragment ions to include in theoretical spectra" help="">
152 <option value="a-B" selected="true">a-B</option> 151 <option value="a-B" selected="true">a-B</option>
153 <option value="a" selected="true">a</option> 152 <option value="a" selected="true">a</option>
154 <option value="b" selected="true">b</option> 153 <option value="b" selected="true">b</option>
155 <option value="c" selected="true">c</option> 154 <option value="c" selected="true">c</option>
156 <option value="d" selected="true">d</option> 155 <option value="d" selected="true">d</option>
160 <option value="z" selected="true">z</option> 159 <option value="z" selected="true">z</option>
161 <expand macro="list_string_san" name="ions"/> 160 <expand macro="list_string_san" name="ions"/>
162 </param> 161 </param>
163 </section> 162 </section>
164 <section name="modifications" title="Modification options" help="" expanded="false"> 163 <section name="modifications" title="Modification options" help="" expanded="false">
165 <param name="variable" argument="-modifications:variable" multiple="true" type="select" optional="true" label="Variable modifications" help=""> 164 <param name="variable" argument="-modifications:variable" type="select" multiple="true" optional="true" label="Variable modifications" help="">
166 <option value="m1Am">m1Am</option> 165 <option value="io6A">io6A</option>
167 <option value="m1Gm">m1Gm</option> 166 <option value="s2U">s2U</option>
168 <option value="m1Im">m1Im</option> 167 <option value="k2C">k2C</option>
169 <option value="m1acp3Y">m1acp3Y</option> 168 <option value="m2Gm">m2Gm</option>
170 <option value="m1A">m1A</option> 169 <option value="Ym">Ym</option>
171 <option value="m1G">m1G</option> 170 <option value="f5Cm">f5Cm</option>
172 <option value="m1I">m1I</option> 171 <option value="Qbase">Qbase</option>
173 <option value="m1Y">m1Y</option> 172 <option value="ac4Cm">ac4Cm</option>
173 <option value="imG-14">imG-14</option>
174 <option value="cm5s2U">cm5s2U</option>
175 <option value="mnm5s2U">mnm5s2U</option>
176 <option value="m227G">m227G</option>
177 <option value="yW-58">yW-58</option>
178 <option value="I">I</option>
179 <option value="g6A">g6A</option>
180 <option value="nm5U">nm5U</option>
181 <option value="m7G">m7G</option>
182 <option value="s2Um">s2Um</option>
183 <option value="Y">Y</option>
184 <option value="hm5C">hm5C</option>
185 <option value="m5U">m5U</option>
186 <option value="preQ0">preQ0</option>
187 <option value="o2yW">o2yW</option>
188 <option value="m5Um">m5Um</option>
189 <option value="preQ1">preQ1</option>
190 <option value="m66Am">m66Am</option>
191 <option value="ac6A">ac6A</option>
192 <option value="ms2io6A">ms2io6A</option>
193 <option value="Am">Am</option>
194 <option value="Im">Im</option>
195 <option value="mnm5U">mnm5U</option>
196 <option value="m22G">m22G</option>
197 <option value="t6A">t6A</option>
198 <option value="m8A">m8A</option>
199 <option value="m7GpppN">m7GpppN</option>
200 <option value="m27GpppN">m27GpppN</option>
201 <option value="m227GpppN">m227GpppN</option>
202 <option value="mpppN">mpppN</option>
174 <option value="m28A">m28A</option> 203 <option value="m28A">m28A</option>
175 <option value="msms2i6A">msms2i6A</option>
176 <option value="ges2U">ges2U</option>
177 <option value="k2C">k2C</option>
178 <option value="m2A">m2A</option>
179 <option value="ms2ct6A">ms2ct6A</option>
180 <option value="ms2io6A">ms2io6A</option>
181 <option value="ms2hn6A">ms2hn6A</option>
182 <option value="ms2i6A">ms2i6A</option>
183 <option value="ms2m6A">ms2m6A</option>
184 <option value="ms2t6A">ms2t6A</option>
185 <option value="se2U">se2U</option>
186 <option value="s2Um">s2Um</option>
187 <option value="s2C">s2C</option>
188 <option value="s2U">s2U</option>
189 <option value="Am">Am</option>
190 <option value="Cm">Cm</option>
191 <option value="Gm">Gm</option>
192 <option value="Im">Im</option>
193 <option value="Ym">Ym</option>
194 <option value="Um">Um</option>
195 <option value="mcmo5Um">mcmo5Um</option>
196 <option value="Ar(p)">Ar(p)</option>
197 <option value="Gr(p)">Gr(p)</option>
198 <option value="(pN)2'3'&gt;p">(pN)2'3'&gt;p</option>
199 <option value="hm5Cm">hm5Cm</option>
200 <option value="m3Um">m3Um</option>
201 <option value="acp3D">acp3D</option> 204 <option value="acp3D">acp3D</option>
202 <option value="acp3Y">acp3Y</option> 205 <option value="acp3Y">acp3Y</option>
203 <option value="acp3U">acp3U</option> 206 <option value="imG">imG</option>
204 <option value="m3C">m3C</option> 207 <option value="D">D</option>
208 <option value="N">N</option>
209 <option value="C+">C+</option>
210 <option value="m27Gm">m27Gm</option>
211 <option value="ho5C">ho5C</option>
212 <option value="inm5U">inm5U</option>
213 <option value="inm5Um">inm5Um</option>
214 <option value="inm5s2U">inm5s2U</option>
215 <option value="pppN">pppN</option>
216 <option value="GpppN">GpppN</option>
217 <option value="CoApN">CoApN</option>
218 <option value="m44C">m44C</option>
219 <option value="acCoApN">acCoApN</option>
220 <option value="malonyl-CoApN">malonyl-CoApN</option>
221 <option value="succinyl-CoApN">succinyl-CoApN</option>
222 <option value="ppN">ppN</option>
223 <option value="NADpN">NADpN</option>
224 <option value="m6t6A">m6t6A</option>
225 <option value="OHyWy">OHyWy</option>
226 <option value="pG(pN)">pG(pN)</option>
227 <option value="ncm5s2U">ncm5s2U</option>
228 <option value="nchm5U">nchm5U</option>
229 <option value="mchm5Um">mchm5Um</option>
230 <option value="pN">pN</option>
231 <option value="ges2U">ges2U</option>
232 <option value="cmnm5ges2U">cmnm5ges2U</option>
233 <option value="mnm5ges2U">mnm5ges2U</option>
234 <option value="nm5ges2U">nm5ges2U</option>
235 <option value="m5D">m5D</option>
236 <option value="mmpN">mmpN</option>
237 <option value="mpN">mpN</option>
238 <option value="5'-OH-N">5'-OH-N</option>
239 <option value="N2'3'cp">N2'3'cp</option>
240 <option value="ct6A">ct6A</option>
241 <option value="hm6A">hm6A</option>
242 <option value="f6A">f6A</option>
243 <option value="cnm5U">cnm5U</option>
244 <option value="mcmo5Um">mcmo5Um</option>
245 <option value="m5C">m5C</option>
246 <option value="ms2ct6A">ms2ct6A</option>
247 <option value="ht6A">ht6A</option>
248 <option value="msms2i6A">msms2i6A</option>
249 <option value="hm5Cm">hm5Cm</option>
250 <option value="pY">pY</option>
251 <option value="pm5C">pm5C</option>
252 <option value="ps2U">ps2U</option>
253 <option value="hn6A">hn6A</option>
254 <option value="pD">pD</option>
255 <option value="pm2G">pm2G</option>
256 <option value="pm66A">pm66A</option>
257 <option value="pGm">pGm</option>
258 <option value="pm5U">pm5U</option>
259 <option value="pm22G">pm22G</option>
260 <option value="pm3U">pm3U</option>
261 <option value="m5Cm">m5Cm</option>
262 <option value="Ar(p)">Ar(p)</option>
263 <option value="pac4C">pac4C</option>
264 <option value="pCm">pCm</option>
265 <option value="pppG">pppG</option>
266 <option value="pm7G">pm7G</option>
267 <option value="pm1A">pm1A</option>
268 <option value="pUm">pUm</option>
269 <option value="pAm">pAm</option>
270 <option value="pm4Cm">pm4Cm</option>
271 <option value="pC2'3'cp">pC2'3'cp</option>
272 <option value="tm5U">tm5U</option>
273 <option value="pm6A">pm6A</option>
274 <option value="pyW">pyW</option>
275 <option value="pm1G">pm1G</option>
276 <option value="pA2'3'cp">pA2'3'cp</option>
277 <option value="ps4U">ps4U</option>
278 <option value="pI">pI</option>
279 <option value="ppG">ppG</option>
280 <option value="pm2A">pm2A</option>
281 <option value="m1G">m1G</option>
282 <option value="pmcm5s2U">pmcm5s2U</option>
283 <option value="cmnm5Um">cmnm5Um</option>
284 <option value="pse2U">pse2U</option>
285 <option value="pt6A">pt6A</option>
286 <option value="pf5C">pf5C</option>
287 <option value="pppA">pppA</option>
288 <option value="pG">pG</option>
289 <option value="pG2'3'cp">pG2'3'cp</option>
290 <option value="pms2i6A">pms2i6A</option>
291 <option value="pcmo5U">pcmo5U</option>
292 <option value="Xm">Xm</option>
293 <option value="pm44C">pm44C</option>
294 <option value="pi6A">pi6A</option>
295 <option value="phm5C">phm5C</option>
296 <option value="pU">pU</option>
297 <option value="pAr(p)">pAr(p)</option>
298 <option value="pac4Cm">pac4Cm</option>
299 <option value="pGp">pGp</option>
300 <option value="m1I">m1I</option>
301 <option value="pU2'3'cp">pU2'3'cp</option>
302 <option value="mcm5U">mcm5U</option>
303 <option value="Gm">Gm</option>
304 <option value="pm4C">pm4C</option>
305 <option value="ncm5Um">ncm5Um</option>
306 <option value="pm5Um">pm5Um</option>
307 <option value="pmnm5U">pmnm5U</option>
308 <option value="pm3C">pm3C</option>
309 <option value="m5s2U">m5s2U</option>
310 <option value="yW">yW</option>
311 <option value="pC">pC</option>
312 <option value="pm6t6A">pm6t6A</option>
313 <option value="f5C">f5C</option>
314 <option value="pAp">pAp</option>
315 <option value="m1Am">m1Am</option>
316 <option value="m1Im">m1Im</option>
317 <option value="ApppN">ApppN</option>
318 <option value="AppppN">AppppN</option>
319 <option value="ApppppN">ApppppN</option>
320 <option value="m6ApppN">m6ApppN</option>
321 <option value="m6AppppN">m6AppppN</option>
322 <option value="m6ApppppN">m6ApppppN</option>
323 <option value="m7GppppN">m7GppppN</option>
324 <option value="Gr(p)">Gr(p)</option>
325 <option value="pm1Am">pm1Am</option>
326 <option value="pm1Gm">pm1Gm</option>
327 <option value="pm1Im">pm1Im</option>
328 <option value="pm1acp3Y">pm1acp3Y</option>
329 <option value="pm1I">pm1I</option>
330 <option value="pm1Y">pm1Y</option>
331 <option value="pk2C">pk2C</option>
332 <option value="ps2C">ps2C</option>
333 <option value="pm3Y">pm3Y</option>
334 <option value="nm5s2U">nm5s2U</option>
335 <option value="pm5Cm">pm5Cm</option>
336 <option value="pmchm5U">pmchm5U</option>
337 <option value="pinm5Um">pinm5Um</option>
338 <option value="pinm5s2U">pinm5s2U</option>
339 <option value="pinm5U">pinm5U</option>
340 <option value="pnm5U">pnm5U</option>
341 <option value="pncm5U">pncm5U</option>
342 <option value="pchm5U">pchm5U</option>
343 <option value="pcmnm5U">pcmnm5U</option>
344 <option value="pcm5U">pcm5U</option>
345 <option value="m2G">m2G</option>
346 <option value="pho5U">pho5U</option>
347 <option value="pmcm5Um">pmcm5Um</option>
348 <option value="pmcm5U">pmcm5U</option>
349 <option value="pmo5U">pmo5U</option>
350 <option value="pm5D">pm5D</option>
351 <option value="pmimG">pmimG</option>
352 <option value="phm5Cm">phm5Cm</option>
353 <option value="pIm">pIm</option>
354 <option value="pYm">pYm</option>
355 <option value="pmcmo5Um">pmcmo5Um</option>
356 <option value="m2A">m2A</option>
357 <option value="pGr(p)">pGr(p)</option>
358 <option value="pm28A">pm28A</option>
359 <option value="pmsms2i6A">pmsms2i6A</option>
360 <option value="pges2U">pges2U</option>
361 <option value="pms2ct6A">pms2ct6A</option>
362 <option value="pms2io6A">pms2io6A</option>
363 <option value="pms2hn6A">pms2hn6A</option>
364 <option value="pms2m6A">pms2m6A</option>
365 <option value="pms2t6A">pms2t6A</option>
366 <option value="ps2Um">ps2Um</option>
367 <option value="pm3Um">pm3Um</option>
368 <option value="pacp3D">pacp3D</option>
369 <option value="pacp3U">pacp3U</option>
370 <option value="pimG-14">pimG-14</option>
371 <option value="pmchm5Um">pmchm5Um</option>
372 <option value="pnm5ges2U">pnm5ges2U</option>
373 <option value="pnm5se2U">pnm5se2U</option>
374 <option value="pnm5s2U">pnm5s2U</option>
375 <option value="pnchm5U">pnchm5U</option>
376 <option value="pncm5Um">pncm5Um</option>
377 <option value="m4Cm">m4Cm</option>
378 <option value="pncm5s2U">pncm5s2U</option>
379 <option value="pcm5s2U">pcm5s2U</option>
380 <option value="pcmnm5Um">pcmnm5Um</option>
381 <option value="pcmnm5ges2U">pcmnm5ges2U</option>
382 <option value="pcmnm5se2U">pcmnm5se2U</option>
383 <option value="pcmnm5s2U">pcmnm5s2U</option>
384 <option value="pcnm5U">pcnm5U</option>
385 <option value="pf5Cm">pf5Cm</option>
386 <option value="pho5C">pho5C</option>
387 <option value="pm5s2U">pm5s2U</option>
388 <option value="m27G">m27G</option>
389 <option value="m22Gm">m22Gm</option>
390 <option value="pmnm5ges2U">pmnm5ges2U</option>
391 <option value="pmnm5se2U">pmnm5se2U</option>
392 <option value="pmnm5s2U">pmnm5s2U</option>
393 <option value="ptm5s2U">ptm5s2U</option>
394 <option value="ptm5U">ptm5U</option>
395 <option value="pyW-86">pyW-86</option>
396 <option value="pyW-72">pyW-72</option>
397 <option value="pyW-58">pyW-58</option>
398 <option value="ppreQ1">ppreQ1</option>
399 <option value="ppreQ0">ppreQ0</option>
400 <option value="m66A">m66A</option>
401 <option value="pm8A">pm8A</option>
402 <option value="pC+">pC+</option>
403 <option value="pG+">pG+</option>
404 <option value="pct6A">pct6A</option>
405 <option value="poQ">poQ</option>
406 <option value="pgalQ">pgalQ</option>
407 <option value="pgluQ">pgluQ</option>
408 <option value="pht6A">pht6A</option>
409 <option value="pOHyW">pOHyW</option>
410 <option value="pimG2">pimG2</option>
411 <option value="gluQ">gluQ</option>
412 <option value="pmanQ">pmanQ</option>
413 <option value="pOHyWy">pOHyWy</option>
414 <option value="pm27Gm">pm27Gm</option>
415 <option value="pQ">pQ</option>
416 <option value="pOHyWx">pOHyWx</option>
417 <option value="pmcmo5U">pmcmo5U</option>
418 <option value="pimG">pimG</option>
419 <option value="pm44Cm">pm44Cm</option>
420 <option value="pm2Gm">pm2Gm</option>
421 <option value="pm22Gm">pm22Gm</option>
422 <option value="ncm5U">ncm5U</option>
423 <option value="pm6Am">pm6Am</option>
424 <option value="pm66Am">pm66Am</option>
425 <option value="pio6A">pio6A</option>
426 <option value="pac6A">pac6A</option>
427 <option value="pf6A">pf6A</option>
428 <option value="pg6A">pg6A</option>
429 <option value="phm6A">phm6A</option>
430 <option value="phn6A">phn6A</option>
431 <option value="cm5U">cm5U</option>
432 <option value="pm27G">pm27G</option>
433 <option value="pm227G">pm227G</option>
434 <option value="pA">pA</option>
435 <option value="cmnm5s2U">cmnm5s2U</option>
436 <option value="cmo5U">cmo5U</option>
205 <option value="m3Y">m3Y</option> 437 <option value="m3Y">m3Y</option>
206 <option value="m3U">m3U</option> 438 <option value="m3U">m3U</option>
207 <option value="imG-14">imG-14</option> 439 <option value="ms2m6A">ms2m6A</option>
440 <option value="Um">Um</option>
441 <option value="ms2i6A">ms2i6A</option>
442 <option value="m3C">m3C</option>
443 <option value="cmnm5se2U">cmnm5se2U</option>
444 <option value="ms2t6A">ms2t6A</option>
445 <option value="i6A">i6A</option>
446 <option value="m3Um">m3Um</option>
447 <option value="mcmo5U">mcmo5U</option>
448 <option value="mimG">mimG</option>
449 <option value="oQ">oQ</option>
450 <option value="preQ1base">preQ1base</option>
451 <option value="nm5se2U">nm5se2U</option>
452 <option value="m1Gm">m1Gm</option>
453 <option value="ho5U">ho5U</option>
454 <option value="Q">Q</option>
455 <option value="xG">xG</option>
456 <option value="mcm5s2U">mcm5s2U</option>
457 <option value="m44Cm">m44Cm</option>
208 <option value="s4U">s4U</option> 458 <option value="s4U">s4U</option>
209 <option value="m5Cm">m5Cm</option> 459 <option value="xC">xC</option>
210 <option value="m5Um">m5Um</option> 460 <option value="yW-86">yW-86</option>
211 <option value="mchm5Um">mchm5Um</option> 461 <option value="xA">xA</option>
462 <option value="chm5U">chm5U</option>
463 <option value="mo5U">mo5U</option>
464 <option value="acp3U">acp3U</option>
465 <option value="xU">xU</option>
466 <option value="yW-72">yW-72</option>
467 <option value="mnm5se2U">mnm5se2U</option>
468 <option value="ms2hn6A">ms2hn6A</option>
469 <option value="m1acp3Y">m1acp3Y</option>
470 <option value="mcm5Um">mcm5Um</option>
471 <option value="ac4C">ac4C</option>
472 <option value="m6Am">m6Am</option>
473 <option value="m1A">m1A</option>
474 <option value="Cm">Cm</option>
212 <option value="mchm5U">mchm5U</option> 475 <option value="mchm5U">mchm5U</option>
213 <option value="inm5s2U">inm5s2U</option> 476 <option value="galQ">galQ</option>
214 <option value="inm5Um">inm5Um</option>
215 <option value="inm5U">inm5U</option>
216 <option value="nm5ges2U">nm5ges2U</option>
217 <option value="nm5se2U">nm5se2U</option>
218 <option value="nm5s2U">nm5s2U</option>
219 <option value="nm5U">nm5U</option>
220 <option value="nchm5U">nchm5U</option>
221 <option value="ncm5s2U">ncm5s2U</option>
222 <option value="ncm5Um">ncm5Um</option>
223 <option value="ncm5U">ncm5U</option>
224 <option value="chm5U">chm5U</option>
225 <option value="cm5s2U">cm5s2U</option>
226 <option value="cmnm5ges2U">cmnm5ges2U</option>
227 <option value="cmnm5se2U">cmnm5se2U</option>
228 <option value="cmnm5s2U">cmnm5s2U</option>
229 <option value="cmnm5Um">cmnm5Um</option>
230 <option value="cmnm5U">cmnm5U</option> 477 <option value="cmnm5U">cmnm5U</option>
231 <option value="cm5U">cm5U</option> 478 <option value="m1Y">m1Y</option>
232 <option value="cnm5U">cnm5U</option> 479 <option value="imG2">imG2</option>
233 <option value="f5Cm">f5Cm</option> 480 <option value="m4C">m4C</option>
234 <option value="f5C">f5C</option> 481 <option value="manQ">manQ</option>
235 <option value="ho5C">ho5C</option>
236 <option value="hm5C">hm5C</option>
237 <option value="ho5U">ho5U</option>
238 <option value="mcm5s2U">mcm5s2U</option>
239 <option value="mcm5Um">mcm5Um</option>
240 <option value="mcm5U">mcm5U</option>
241 <option value="mo5U">mo5U</option>
242 <option value="m5s2U">m5s2U</option>
243 <option value="mnm5ges2U">mnm5ges2U</option>
244 <option value="mnm5se2U">mnm5se2U</option>
245 <option value="mnm5s2U">mnm5s2U</option>
246 <option value="mnm5U">mnm5U</option>
247 <option value="m5C">m5C</option>
248 <option value="m5D">m5D</option>
249 <option value="m5U">m5U</option>
250 <option value="tm5s2U">tm5s2U</option> 482 <option value="tm5s2U">tm5s2U</option>
251 <option value="tm5U">tm5U</option> 483 <option value="s2C">s2C</option>
252 <option value="CoA(pN)">CoA(pN)</option> 484 <option value="OHyWx">OHyWx</option>
253 <option value="acCoA(pN)">acCoA(pN)</option> 485 <option value="se2U">se2U</option>
254 <option value="malonyl-CoA(pN)">malonyl-CoA(pN)</option> 486 <option value="preQ0base">preQ0base</option>
255 <option value="succinyl-CoA(pN)">succinyl-CoA(pN)</option>
256 <option value="p(pN)">p(pN)</option>
257 <option value="5'-OH-N">5'-OH-N</option>
258 <option value="(pN)">(pN)</option>
259 <option value="NAD(pN)">NAD(pN)</option>
260 <option value="pp(pN)">pp(pN)</option>
261 <option value="yW-86">yW-86</option>
262 <option value="yW-72">yW-72</option>
263 <option value="yW-58">yW-58</option>
264 <option value="preQ1tRNA">preQ1tRNA</option>
265 <option value="preQ0tRNA">preQ0tRNA</option>
266 <option value="m7G">m7G</option>
267 <option value="m7Gpp(pN)">m7Gpp(pN)</option>
268 <option value="m8A">m8A</option>
269 <option value="m2Gm">m2Gm</option>
270 <option value="m27Gm">m27Gm</option>
271 <option value="m27G">m27G</option>
272 <option value="m27Gpp(pN)">m27Gpp(pN)</option>
273 <option value="m22Gm">m22Gm</option>
274 <option value="m227G">m227G</option>
275 <option value="m227Gpp(pN)">m227Gpp(pN)</option>
276 <option value="m22G">m22G</option>
277 <option value="m2G">m2G</option>
278 <option value="m4Cm">m4Cm</option>
279 <option value="m44Cm">m44Cm</option>
280 <option value="m44C">m44C</option>
281 <option value="ac4Cm">ac4Cm</option>
282 <option value="ac4C">ac4C</option>
283 <option value="m4C">m4C</option>
284 <option value="m6Am">m6Am</option>
285 <option value="m66Am">m66Am</option>
286 <option value="m66A">m66A</option>
287 <option value="io6A">io6A</option>
288 <option value="ac6A">ac6A</option>
289 <option value="f6A">f6A</option>
290 <option value="g6A">g6A</option>
291 <option value="hm6A">hm6A</option>
292 <option value="hn6A">hn6A</option>
293 <option value="i6A">i6A</option>
294 <option value="m6t6A">m6t6A</option>
295 <option value="m6A">m6A</option> 487 <option value="m6A">m6A</option>
296 <option value="t6A">t6A</option> 488 <option value="OHyW">OHyW</option>
297 <option value="Qbase">Qbase</option> 489 <option value="xX">xX</option>
298 <option value="C+">C+</option>
299 <option value="mm(pN)">mm(pN)</option>
300 <option value="m(pN)">m(pN)</option>
301 <option value="G+">G+</option> 490 <option value="G+">G+</option>
302 <option value="ct6A">ct6A</option>
303 <option value="D">D</option>
304 <option value="oQ">oQ</option>
305 <option value="galQ">galQ</option>
306 <option value="mpp(pN)">mpp(pN)</option>
307 <option value="gluQ">gluQ</option>
308 <option value="pG(pN)">pG(pN)</option>
309 <option value="Gpp(pN)">Gpp(pN)</option>
310 <option value="ht6A">ht6A</option>
311 <option value="OHyW">OHyW</option>
312 <option value="I">I</option>
313 <option value="imG2">imG2</option>
314 <option value="manQ">manQ</option>
315 <option value="OHyWy">OHyWy</option>
316 <option value="mimG">mimG</option>
317 <option value="o2yW">o2yW</option>
318 <option value="preQ0base">preQ0base</option>
319 <option value="preQ1base">preQ1base</option>
320 <option value="Y">Y</option>
321 <option value="Q">Q</option>
322 <option value="OHyWx">OHyWx</option>
323 <option value="Xm">Xm</option>
324 <option value="xX">xX</option>
325 <option value="xA">xA</option>
326 <option value="xC">xC</option>
327 <option value="xG">xG</option>
328 <option value="xU">xU</option>
329 <option value="N">N</option>
330 <option value="cmo5U">cmo5U</option>
331 <option value="mcmo5U">mcmo5U</option>
332 <option value="yW">yW</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>
339 <option value="3'-p">3'-p</option> 491 <option value="3'-p">3'-p</option>
340 <option value="5'-p">5'-p</option> 492 <option value="5'-p">5'-p</option>
493 <option value="5'-p*">5'-p*</option>
494 <option value="3'-c">3'-c</option>
341 <option value="mA">mA</option> 495 <option value="mA">mA</option>
342 <option value="mC">mC</option> 496 <option value="mC">mC</option>
343 <option value="mG">mG</option> 497 <option value="mG">mG</option>
344 <option value="mU">mU</option> 498 <option value="mU">mU</option>
345 <option value="sU">sU</option> 499 <option value="sU">sU</option>
363 <option value="mmC?">mmC?</option> 517 <option value="mmC?">mmC?</option>
364 <option value="mmG?">mmG?</option> 518 <option value="mmG?">mmG?</option>
365 <option value="mmmG?">mmmG?</option> 519 <option value="mmmG?">mmmG?</option>
366 <option value="ac4C/f5Cm?">ac4C/f5Cm?</option> 520 <option value="ac4C/f5Cm?">ac4C/f5Cm?</option>
367 <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option> 521 <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option>
522 <option value="dA">dA</option>
523 <option value="dC">dC</option>
524 <option value="dG">dG</option>
525 <option value="dU">dU</option>
526 <option value="dT">dT</option>
527 <option value="A*">A*</option>
528 <option value="C*">C*</option>
529 <option value="G*">G*</option>
530 <option value="U*">U*</option>
531 <option value="dA*">dA*</option>
532 <option value="dC*">dC*</option>
533 <option value="dG*">dG*</option>
534 <option value="dU*">dU*</option>
535 <option value="dT*">dT*</option>
368 <expand macro="list_string_san" name="variable"/> 536 <expand macro="list_string_san" name="variable"/>
369 </param> 537 </param>
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=""/> 538 <param name="variable_max_per_oligo" argument="-modifications:variable_max_per_oligo" type="integer" value="2" label="Maximum number of residues carrying a variable modification per candidate oligonucleotide" help=""/>
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'"/> 539 <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'"/>
372 </section> 540 </section>
373 <section name="oligo" title="Oligonucleotide (digestion) options (ignored if 'digest' input is used)" help="" expanded="false"> 541 <section name="oligo" title="Oligonucleotide (digestion) options (ignored if 'digest' input is used)" help="" expanded="false">
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=""/> 542 <param name="min_size" argument="-oligo:min_size" type="integer" value="5" label="Minimum size an oligonucleotide must have after digestion to be considered in the search" 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=""/> 543 <param name="max_size" argument="-oligo:max_size" type="integer" value="0" label="Maximum size an oligonucleotide must have after digestion to be considered in the search, leave at 0 for no limit" help=""/>
376 <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" optional="true" value="1" label="Number of missed cleavages" help=""/> 544 <param name="missed_cleavages" argument="-oligo:missed_cleavages" type="integer" value="1" label="Number of missed cleavages" help=""/>
377 <param name="enzyme" argument="-oligo:enzyme" type="select" optional="true" label="The enzyme used for RNA digestion" help=""> 545 <param name="enzyme" argument="-oligo:enzyme" type="select" label="The enzyme used for RNA digestion" help="">
378 <option value="RNase_T1">RNase_T1</option> 546 <option value="RNase_A">RNase_A</option>
379 <option value="cusativin">cusativin</option> 547 <option value="RNase_MC1">RNase_MC1</option>
380 <option value="RNase_H">RNase_H</option> 548 <option value="RNase_H">RNase_H</option>
381 <option value="mazF">mazF</option> 549 <option value="mazF">mazF</option>
550 <option value="cusativin">cusativin</option>
551 <option value="RNase_T1">RNase_T1</option>
382 <option value="colicin_E5">colicin_E5</option> 552 <option value="colicin_E5">colicin_E5</option>
383 <option value="no cleavage" selected="true">no cleavage</option> 553 <option value="no cleavage" selected="true">no cleavage</option>
554 <option value="unspecific cleavage">unspecific cleavage</option>
384 <option value="RNase_U2">RNase_U2</option> 555 <option value="RNase_U2">RNase_U2</option>
385 <option value="RNase_A">RNase_A</option>
386 <option value="RNase_MC1">RNase_MC1</option>
387 <option value="unspecific cleavage">unspecific cleavage</option>
388 <expand macro="list_string_san" name="enzyme"/> 556 <expand macro="list_string_san" name="enzyme"/>
389 </param> 557 </param>
390 </section> 558 </section>
391 <section name="report" title="Reporting Options" help="" expanded="false"> 559 <section name="report" title="Reporting Options" help="" expanded="false">
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=""/> 560 <param name="top_hits" argument="-report:top_hits" type="integer" min="0" value="1" label="Maximum number of top-scoring hits per spectrum that are reported ('0' for all hits)" help=""/>
393 </section> 561 </section>
394 <section name="fdr" title="False Discovery Rate options" help="" expanded="false"> 562 <section name="fdr" title="False Discovery Rate options" help="" expanded="false">
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"> 563 <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">
396 <expand macro="list_string_san" name="decoy_pattern"/> 564 <expand macro="list_string_san" name="decoy_pattern"/>
397 </param> 565 </param>
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=""/> 566 <param name="cutoff" argument="-fdr:cutoff" type="float" 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=""/>
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=""/> 567 <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=""/>
400 </section> 568 </section>
401 <expand macro="adv_opts_macro"> 569 <expand macro="adv_opts_macro">
402 <param argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/> 570 <param argument="-decharge_ms2" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Decharge the MS2 spectra for scoring" help=""/>
403 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 571 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
404 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 572 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
405 <expand macro="list_string_san" name="test"/> 573 <expand macro="list_string_san" name="test"/>
406 </param> 574 </param>
407 </expand> 575 </expand>
408 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 576 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
409 <option value="id_out_FLAG">id_out (Output file: idXML (for visualization in TOPPView))</option> 577 <option value="id_out_FLAG">id_out (Output file: idXML (for visualization in TOPPView))</option>
437 </data> 605 </data>
438 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 606 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
439 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 607 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
440 </data> 608 </data>
441 </outputs> 609 </outputs>
442 <tests><!-- UTILS_NucleicAcidSearchEngine_1 --> 610 <tests>
611 <!-- TOPP_NucleicAcidSearchEngine_1 -->
443 <test expect_num_outputs="5"> 612 <test expect_num_outputs="5">
444 <section name="adv_opts"> 613 <section name="adv_opts">
445 <param name="decharge_ms2" value="false"/> 614 <param name="decharge_ms2" value="false"/>
446 <param name="force" value="false"/> 615 <param name="force" value="false"/>
447 <param name="test" value="true"/> 616 <param name="test" value="true"/>
448 </section> 617 </section>
449 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> 618 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
450 <param name="database" value="NucleicAcidSearchEngine_1.fasta"/> 619 <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"/> 620 <output name="out" value="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"/> 621 <output name="id_out" value="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"/> 622 <output name="db_out" value="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"/> 623 <output name="digest_out" value="NucleicAcidSearchEngine_1_digest.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
455 <section name="precursor"> 624 <section name="precursor">
456 <param name="mass_tolerance" value="5.0"/> 625 <param name="mass_tolerance" value="5.0"/>
457 <param name="mass_tolerance_unit" value="ppm"/> 626 <param name="mass_tolerance_unit" value="ppm"/>
458 <param name="min_charge" value="-2"/> 627 <param name="min_charge" value="-2"/>
459 <param name="max_charge" value="-14"/> 628 <param name="max_charge" value="-14"/>
460 <param name="include_unknown_charge" value="true"/> 629 <param name="include_unknown_charge" value="true"/>
461 <param name="use_avg_mass" value="false"/> 630 <param name="use_avg_mass" value="false"/>
462 <param name="use_adducts" value="false"/> 631 <param name="use_adducts" value="true"/>
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;"/> 632 <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"/> 633 <param name="isotopes" value="0 1 2"/>
465 </section> 634 </section>
466 <section name="fragment"> 635 <section name="fragment">
467 <param name="mass_tolerance" value="5.0"/> 636 <param name="mass_tolerance" value="5.0"/>
468 <param name="mass_tolerance_unit" value="ppm"/> 637 <param name="mass_tolerance_unit" value="ppm"/>
469 <param name="ions" value="a-B,c,w,y"/> 638 <param name="ions" value="a-B,c,w,y"/>
470 </section> 639 </section>
471 <section name="modifications"> 640 <section name="modifications">
472 <param name="variable"/>
473 <param name="variable_max_per_oligo" value="2"/> 641 <param name="variable_max_per_oligo" value="2"/>
474 <param name="resolve_ambiguities" value="false"/> 642 <param name="resolve_ambiguities" value="false"/>
475 </section> 643 </section>
476 <section name="oligo"> 644 <section name="oligo">
477 <param name="min_size" value="5"/> 645 <param name="min_size" value="5"/>
491 <output name="ctd_out" ftype="xml"> 659 <output name="ctd_out" ftype="xml">
492 <assert_contents> 660 <assert_contents>
493 <is_valid_xml/> 661 <is_valid_xml/>
494 </assert_contents> 662 </assert_contents>
495 </output> 663 </output>
664 <assert_stdout>
665 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
666 </assert_stdout>
496 </test> 667 </test>
497 <!-- UTILS_NucleicAcidSearchEngine_2 --> 668 <!-- TOPP_NucleicAcidSearchEngine_2 -->
498 <test expect_num_outputs="4"> 669 <test expect_num_outputs="4">
499 <section name="adv_opts"> 670 <section name="adv_opts">
500 <param name="decharge_ms2" value="false"/> 671 <param name="decharge_ms2" value="false"/>
501 <param name="force" value="false"/> 672 <param name="force" value="false"/>
502 <param name="test" value="true"/> 673 <param name="test" value="true"/>
503 </section> 674 </section>
504 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/> 675 <param name="in" value="NucleicAcidSearchEngine_1.mzML"/>
505 <param name="digest" value="NucleicAcidSearchEngine_1_digest.oms"/> 676 <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"/> 677 <output name="out" value="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"/> 678 <output name="id_out" value="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"/> 679 <output name="db_out" value="NucleicAcidSearchEngine_23_out.tmp" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
509 <section name="precursor"> 680 <section name="precursor">
510 <param name="mass_tolerance" value="5.0"/> 681 <param name="mass_tolerance" value="5.0"/>
511 <param name="mass_tolerance_unit" value="ppm"/> 682 <param name="mass_tolerance_unit" value="ppm"/>
512 <param name="min_charge" value="-2"/> 683 <param name="min_charge" value="-2"/>
513 <param name="max_charge" value="-14"/> 684 <param name="max_charge" value="-14"/>
514 <param name="include_unknown_charge" value="true"/> 685 <param name="include_unknown_charge" value="true"/>
515 <param name="use_avg_mass" value="false"/> 686 <param name="use_avg_mass" value="false"/>
516 <param name="use_adducts" value="false"/> 687 <param name="use_adducts" value="true"/>
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;"/> 688 <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"/> 689 <param name="isotopes" value="0 1 2"/>
519 </section> 690 </section>
520 <section name="fragment"> 691 <section name="fragment">
521 <param name="mass_tolerance" value="5.0"/> 692 <param name="mass_tolerance" value="5.0"/>
522 <param name="mass_tolerance_unit" value="ppm"/> 693 <param name="mass_tolerance_unit" value="ppm"/>
523 <param name="ions" value="a-B,c,w,y"/> 694 <param name="ions" value="a-B,c,w,y"/>
524 </section> 695 </section>
525 <section name="modifications"> 696 <section name="modifications">
526 <param name="variable"/>
527 <param name="variable_max_per_oligo" value="2"/> 697 <param name="variable_max_per_oligo" value="2"/>
528 <param name="resolve_ambiguities" value="false"/> 698 <param name="resolve_ambiguities" value="false"/>
529 </section> 699 </section>
530 <section name="oligo"> 700 <section name="oligo">
531 <param name="min_size" value="5"/> 701 <param name="min_size" value="5"/>
545 <output name="ctd_out" ftype="xml"> 715 <output name="ctd_out" ftype="xml">
546 <assert_contents> 716 <assert_contents>
547 <is_valid_xml/> 717 <is_valid_xml/>
548 </assert_contents> 718 </assert_contents>
549 </output> 719 </output>
720 <assert_stdout>
721 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
722 </assert_stdout>
550 </test> 723 </test>
551 </tests> 724 </tests>
552 <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra. 725 <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra.
553 726
554 727
555 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_NucleicAcidSearchEngine.html]]></help> 728 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_NucleicAcidSearchEngine.html]]></help>
556 <expand macro="references"/> 729 <expand macro="references"/>
557 </tool> 730 </tool>