Mercurial > repos > galaxyp > openms_nucleicacidsearchengine

comparison NucleicAcidSearchEngine.xml @ 0:fe6eddc2e756 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:47:24 -0400
parents
children 00b91aaec050
comparison
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-1:000000000000 0:fe6eddc2e756
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="NucleicAcidSearchEngine" name="NucleicAcidSearchEngine" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Annotate nucleic acid identifications to MS/MS spectra.</description>
6 <macros>
7 <token name="@EXECUTABLE@">NucleicAcidSearchEngine</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($in.ext)' &&
21 mkdir database &&
22 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
23 mkdir out &&
24 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
25 mkdir id_out &&
26 #end if
27 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
28 mkdir lfq_out &&
29 #end if
30 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
31 mkdir theo_ms2_out &&
32 #end if
33 #if "exp_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 mkdir exp_ms2_out &&
35 #end if
36
37 ## Main program call
38
39 set -o pipefail &&
40 @EXECUTABLE@ -write_ctd ./ &&
41 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
42 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
43 -in
44 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
45 -database
46 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
47 -out
48 'out/output.${gxy2omsext("mztab")}'
49 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
50 -id_out
51 'id_out/output.${gxy2omsext("idxml")}'
52 #end if
53 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
54 -lfq_out
55 'lfq_out/output.${gxy2omsext("tabular")}'
56 #end if
57 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
58 -theo_ms2_out
59 'theo_ms2_out/output.${gxy2omsext("mzml")}'
60 #end if
61 #if "exp_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
62 -exp_ms2_out
63 'exp_ms2_out/output.${gxy2omsext("mzml")}'
64 #end if
65 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
66 | tee '$stdout'
67 #end if
68
69 ## Postprocessing
70 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
71 #if "id_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
72 && mv 'id_out/output.${gxy2omsext("idxml")}' '$id_out'
73 #end if
74 #if "lfq_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
75 && mv 'lfq_out/output.${gxy2omsext("tabular")}' '$lfq_out'
76 #end if
77 #if "theo_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
78 && mv 'theo_ms2_out/output.${gxy2omsext("mzml")}' '$theo_ms2_out'
79 #end if
80 #if "exp_ms2_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
81 && mv 'exp_ms2_out/output.${gxy2omsext("mzml")}' '$exp_ms2_out'
82 #end if
83 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
84 && mv '@EXECUTABLE@.ctd' '$ctd_out'
85 #end if]]></command>
86 <configfiles>
87 <inputs name="args_json" data_style="paths"/>
88 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
89 </configfiles>
90 <inputs>
91 <param name="in" 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)"/>
93 <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=""/>
95 <param name="mass_tolerance_unit" argument="-precursor:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
96 <option value="Da">Da</option>
97 <option value="ppm" selected="true">ppm</option>
98 <expand macro="list_string_san"/>
99 </param>
100 <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=""/>
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=""/>
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=""/>
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=""/>
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)">
106 <expand macro="list_string_val"/>
107 <expand macro="list_string_san"/>
108 </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)">
110 <expand macro="list_integer_valsan"/>
111 </param>
112 </section>
113 <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=""/>
115 <param name="mass_tolerance_unit" argument="-fragment:mass_tolerance_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
116 <option value="Da">Da</option>
117 <option value="ppm" selected="true">ppm</option>
118 <expand macro="list_string_san"/>
119 </param>
120 <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>
122 <option value="a" selected="true">a</option>
123 <option value="b" selected="true">b</option>
124 <option value="c" selected="true">c</option>
125 <option value="d" selected="true">d</option>
126 <option value="w" selected="true">w</option>
127 <option value="x" selected="true">x</option>
128 <option value="y" selected="true">y</option>
129 <option value="z" selected="true">z</option>
130 <expand macro="list_string_san"/>
131 </param>
132 </section>
133 <section name="modifications" title="Modifications Options" help="" expanded="false">
134 <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>
137 <option value="m1Gm">m1Gm</option>
138 <option value="m1Im">m1Im</option>
139 <option value="m1acp3Y">m1acp3Y</option>
140 <option value="m1A">m1A</option>
141 <option value="m1G">m1G</option>
142 <option value="m1I">m1I</option>
143 <option value="m1Y">m1Y</option>
144 <option value="m28A">m28A</option>
145 <option value="msms2i6A">msms2i6A</option>
146 <option value="ges2U">ges2U</option>
147 <option value="k2C">k2C</option>
148 <option value="m2A">m2A</option>
149 <option value="ms2ct6A">ms2ct6A</option>
150 <option value="ms2io6A">ms2io6A</option>
151 <option value="ms2hn6A">ms2hn6A</option>
152 <option value="ms2i6A">ms2i6A</option>
153 <option value="ms2m6A">ms2m6A</option>
154 <option value="ms2t6A">ms2t6A</option>
155 <option value="se2U">se2U</option>
156 <option value="s2Um">s2Um</option>
157 <option value="s2C">s2C</option>
158 <option value="s2U">s2U</option>
159 <option value="Am">Am</option>
160 <option value="Cm">Cm</option>
161 <option value="Gm">Gm</option>
162 <option value="Im">Im</option>
163 <option value="Ym">Ym</option>
164 <option value="Um">Um</option>
165 <option value="mcmo5Um">mcmo5Um</option>
166 <option value="Ar(p)">Ar(p)</option>
167 <option value="Gr(p)">Gr(p)</option>
168 <option value="(pN)2'3'&gt;p">(pN)2'3'&gt;p</option>
169 <option value="hm5Cm">hm5Cm</option>
170 <option value="m3Um">m3Um</option>
171 <option value="acp3D">acp3D</option>
172 <option value="acp3Y">acp3Y</option>
173 <option value="acp3U">acp3U</option>
174 <option value="m3C">m3C</option>
175 <option value="m3Y">m3Y</option>
176 <option value="m3U">m3U</option>
177 <option value="imG-14">imG-14</option>
178 <option value="s4U">s4U</option>
179 <option value="m5Cm">m5Cm</option>
180 <option value="m5Um">m5Um</option>
181 <option value="mchm5Um">mchm5Um</option>
182 <option value="mchm5U">mchm5U</option>
183 <option value="inm5s2U">inm5s2U</option>
184 <option value="inm5Um">inm5Um</option>
185 <option value="inm5U">inm5U</option>
186 <option value="nm5ges2U">nm5ges2U</option>
187 <option value="nm5se2U">nm5se2U</option>
188 <option value="nm5s2U">nm5s2U</option>
189 <option value="nm5U">nm5U</option>
190 <option value="nchm5U">nchm5U</option>
191 <option value="ncm5s2U">ncm5s2U</option>
192 <option value="ncm5Um">ncm5Um</option>
193 <option value="ncm5U">ncm5U</option>
194 <option value="chm5U">chm5U</option>
195 <option value="cm5s2U">cm5s2U</option>
196 <option value="cmnm5ges2U">cmnm5ges2U</option>
197 <option value="cmnm5se2U">cmnm5se2U</option>
198 <option value="cmnm5s2U">cmnm5s2U</option>
199 <option value="cmnm5Um">cmnm5Um</option>
200 <option value="cmnm5U">cmnm5U</option>
201 <option value="cm5U">cm5U</option>
202 <option value="cnm5U">cnm5U</option>
203 <option value="f5Cm">f5Cm</option>
204 <option value="f5C">f5C</option>
205 <option value="ho5C">ho5C</option>
206 <option value="hm5C">hm5C</option>
207 <option value="ho5U">ho5U</option>
208 <option value="mcm5s2U">mcm5s2U</option>
209 <option value="mcm5Um">mcm5Um</option>
210 <option value="mcm5U">mcm5U</option>
211 <option value="mo5U">mo5U</option>
212 <option value="m5s2U">m5s2U</option>
213 <option value="mnm5ges2U">mnm5ges2U</option>
214 <option value="mnm5se2U">mnm5se2U</option>
215 <option value="mnm5s2U">mnm5s2U</option>
216 <option value="mnm5U">mnm5U</option>
217 <option value="m5C">m5C</option>
218 <option value="m5D">m5D</option>
219 <option value="m5U">m5U</option>
220 <option value="tm5s2U">tm5s2U</option>
221 <option value="tm5U">tm5U</option>
222 <option value="CoA(pN)">CoA(pN)</option>
223 <option value="acCoA(pN)">acCoA(pN)</option>
224 <option value="malonyl-CoA(pN)">malonyl-CoA(pN)</option>
225 <option value="succinyl-CoA(pN)">succinyl-CoA(pN)</option>
226 <option value="p(pN)">p(pN)</option>
227 <option value="5'-OH-N">5'-OH-N</option>
228 <option value="(pN)">(pN)</option>
229 <option value="NAD(pN)">NAD(pN)</option>
230 <option value="pp(pN)">pp(pN)</option>
231 <option value="yW-86">yW-86</option>
232 <option value="yW-72">yW-72</option>
233 <option value="yW-58">yW-58</option>
234 <option value="preQ1tRNA">preQ1tRNA</option>
235 <option value="preQ0tRNA">preQ0tRNA</option>
236 <option value="m7G">m7G</option>
237 <option value="m7Gpp(pN)">m7Gpp(pN)</option>
238 <option value="m8A">m8A</option>
239 <option value="m2Gm">m2Gm</option>
240 <option value="m27Gm">m27Gm</option>
241 <option value="m27G">m27G</option>
242 <option value="m27Gpp(pN)">m27Gpp(pN)</option>
243 <option value="m22Gm">m22Gm</option>
244 <option value="m227G">m227G</option>
245 <option value="m227Gpp(pN)">m227Gpp(pN)</option>
246 <option value="m22G">m22G</option>
247 <option value="m2G">m2G</option>
248 <option value="m4Cm">m4Cm</option>
249 <option value="m44Cm">m44Cm</option>
250 <option value="m44C">m44C</option>
251 <option value="ac4Cm">ac4Cm</option>
252 <option value="ac4C">ac4C</option>
253 <option value="m4C">m4C</option>
254 <option value="m6Am">m6Am</option>
255 <option value="m66Am">m66Am</option>
256 <option value="m66A">m66A</option>
257 <option value="io6A">io6A</option>
258 <option value="ac6A">ac6A</option>
259 <option value="f6A">f6A</option>
260 <option value="g6A">g6A</option>
261 <option value="hm6A">hm6A</option>
262 <option value="hn6A">hn6A</option>
263 <option value="i6A">i6A</option>
264 <option value="m6t6A">m6t6A</option>
265 <option value="m6A">m6A</option>
266 <option value="t6A">t6A</option>
267 <option value="Qbase">Qbase</option>
268 <option value="C+">C+</option>
269 <option value="mm(pN)">mm(pN)</option>
270 <option value="m(pN)">m(pN)</option>
271 <option value="G+">G+</option>
272 <option value="ct6A">ct6A</option>
273 <option value="D">D</option>
274 <option value="oQ">oQ</option>
275 <option value="galQ">galQ</option>
276 <option value="mpp(pN)">mpp(pN)</option>
277 <option value="gluQ">gluQ</option>
278 <option value="pG(pN)">pG(pN)</option>
279 <option value="Gpp(pN)">Gpp(pN)</option>
280 <option value="ht6A">ht6A</option>
281 <option value="OHyW">OHyW</option>
282 <option value="I">I</option>
283 <option value="imG2">imG2</option>
284 <option value="manQ">manQ</option>
285 <option value="OHyWy">OHyWy</option>
286 <option value="mimG">mimG</option>
287 <option value="o2yW">o2yW</option>
288 <option value="preQ0base">preQ0base</option>
289 <option value="preQ1base">preQ1base</option>
290 <option value="Y">Y</option>
291 <option value="Q">Q</option>
292 <option value="OHyWx">OHyWx</option>
293 <option value="Xm">Xm</option>
294 <option value="xX">xX</option>
295 <option value="xA">xA</option>
296 <option value="xC">xC</option>
297 <option value="xG">xG</option>
298 <option value="xU">xU</option>
299 <option value="N">N</option>
300 <option value="cmo5U">cmo5U</option>
301 <option value="mcmo5U">mcmo5U</option>
302 <option value="yW">yW</option>
303 <option value="imG">imG</option>
304 <option value="3'-p">3'-p</option>
305 <option value="5'-p">5'-p</option>
306 <option value="mA">mA</option>
307 <option value="mC">mC</option>
308 <option value="mG">mG</option>
309 <option value="mU">mU</option>
310 <option value="sU">sU</option>
311 <option value="mmA">mmA</option>
312 <option value="mAm">mAm</option>
313 <option value="mCm">mCm</option>
314 <option value="mGm">mGm</option>
315 <option value="mUm">mUm</option>
316 <option value="cmo5U/chm5U">cmo5U/chm5U</option>
317 <option value="mchm5U/mcmo5U">mchm5U/mcmo5U</option>
318 <option value="mchm5Um/mcmo5Um">mchm5Um/mcmo5Um</option>
319 <option value="m6t6A/hn6A">m6t6A/hn6A</option>
320 <option value="galQ/manQ">galQ/manQ</option>
321 <option value="mA?">mA?</option>
322 <option value="mC?">mC?</option>
323 <option value="mG?">mG?</option>
324 <option value="mU?">mU?</option>
325 <option value="mI?">mI?</option>
326 <option value="msU?">msU?</option>
327 <option value="mmA?">mmA?</option>
328 <option value="mmC?">mmC?</option>
329 <option value="mmG?">mmG?</option>
330 <option value="mmmG?">mmmG?</option>
331 <option value="ac4C/f5Cm?">ac4C/f5Cm?</option>
332 <option value="acp3U/cmnm5Um?">acp3U/cmnm5Um?</option>
333 <expand macro="list_string_san"/>
334 </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=""/>
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'"/>
337 </section>
338 <section name="oligo" title="Oligonucleotide Options" 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=""/>
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=""/>
341 <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="">
343 <option value="RNase_T1">RNase_T1</option>
344 <option value="cusativin">cusativin</option>
345 <option value="RNase_U2">RNase_U2</option>
346 <option value="RNase_A">RNase_A</option>
347 <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>
351 <expand macro="list_string_san"/>
352 </param>
353 </section>
354 <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=""/>
356 </section>
357 <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">
359 <expand macro="list_string_san"/>
360 </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=""/>
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=""/>
363 </section>
364 <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=""/>
366 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite 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="">
368 <expand macro="list_string_san"/>
369 </param>
370 </expand>
371 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
372 <option value="id_out_FLAG">id_out (Do not score hits to decoy sequences and remove them when filtering)</option>
373 <option value="lfq_out_FLAG">lfq_out (Do not score hits to decoy sequences and remove them when filtering)</option>
374 <option value="theo_ms2_out_FLAG">theo_ms2_out (Do not score hits to decoy sequences and remove them when filtering)</option>
375 <option value="exp_ms2_out_FLAG">exp_ms2_out (Do not score hits to decoy sequences and remove them when filtering)</option>
376 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
377 </param>
378 </inputs>
379 <outputs>
380 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
381 <data name="id_out" label="${tool.name} on ${on_string}: id_out" format="idxml">
382 <filter>OPTIONAL_OUTPUTS is not None and "id_out_FLAG" in OPTIONAL_OUTPUTS</filter>
383 </data>
384 <data name="lfq_out" label="${tool.name} on ${on_string}: lfq_out" format="tabular">
385 <filter>OPTIONAL_OUTPUTS is not None and "lfq_out_FLAG" in OPTIONAL_OUTPUTS</filter>
386 </data>
387 <data name="theo_ms2_out" label="${tool.name} on ${on_string}: theo_ms2_out" format="mzml">
388 <filter>OPTIONAL_OUTPUTS is not None and "theo_ms2_out_FLAG" in OPTIONAL_OUTPUTS</filter>
389 </data>
390 <data name="exp_ms2_out" label="${tool.name} on ${on_string}: exp_ms2_out" format="mzml">
391 <filter>OPTIONAL_OUTPUTS is not None and "exp_ms2_out_FLAG" in OPTIONAL_OUTPUTS</filter>
392 </data>
393 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
394 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
395 </data>
396 </outputs>
397 <tests>
398 <expand macro="autotest_NucleicAcidSearchEngine"/>
399 <expand macro="manutest_NucleicAcidSearchEngine"/>
400 </tests>
401 <help><![CDATA[Annotate nucleic acid identifications to MS/MS spectra.
402
403
404 For more information, visit http://www.openms.de/documentation/UTILS_NucleicAcidSearchEngine.html]]></help>
405 <expand macro="references"/>
406 </tool>