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comparison MascotAdapter.xml @ 9:fb751f9c050b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:07:35 +0000
parents fd960d61b64d
children 57fb2083a8cb
comparison
equal deleted inserted replaced
8:e52d5d3bfc62 9:fb751f9c050b
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="MascotAdapter" name="MascotAdapter" version="2.3.0"> 4 <tool id="MascotAdapter" name="MascotAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Annotates MS/MS spectra using Mascot.</description> 5 <description>Annotates MS/MS spectra using Mascot.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MascotAdapter</token> 7 <token name="@EXECUTABLE@">MascotAdapter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MascotAdapter 15 @EXT_FOO@
14 16 #import re
15 #if $param_in: 17
16 -in $param_in 18 ## Preprocessing
17 #end if 19 mkdir in &&
18 #if $param_out: 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 -out $param_out 21 mkdir out &&
20 #end if 22
21 #if $param_mascot_in: 23 ## Main program call
22 -mascot_in 24
23 #end if 25 set -o pipefail &&
24 #if $param_mascot_out: 26 @EXECUTABLE@ -write_ctd ./ &&
25 -mascot_out 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
26 #end if 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
27 #if $param_instrument: 29 -in
28 -instrument "$param_instrument" 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
29 #end if 31 -out
30 #if $param_precursor_mass_tolerance: 32 'out/output.${gxy2omsext("idxml")}'
31 -precursor_mass_tolerance $param_precursor_mass_tolerance 33
32 #end if 34 ## Postprocessing
33 #if $param_peak_mass_tolerance: 35 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
34 -peak_mass_tolerance $param_peak_mass_tolerance 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
35 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
36 #if $param_taxonomy: 38 #end if]]></command>
37 -taxonomy 39 <configfiles>
38 #if " " in str($param_taxonomy): 40 <inputs name="args_json" data_style="paths"/>
39 "$param_taxonomy" 41 <configfile name="hardcoded_json"><![CDATA[{"mascot_directory": "TODO", "temp_data_directory": "\$TMP_DIR", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 #else 42 </configfiles>
41 $param_taxonomy
42 #end if
43 #end if
44
45 #if $rep_param_modifications:
46 -modifications
47 #for token in $rep_param_modifications:
48 #if " " in str(token):
49 "$token.param_modifications"
50 #else
51 $token.param_modifications
52 #end if
53 #end for
54 #end if
55
56 #if $rep_param_variable_modifications:
57 -variable_modifications
58 #for token in $rep_param_variable_modifications:
59 #if " " in str(token):
60 "$token.param_variable_modifications"
61 #else
62 $token.param_variable_modifications
63 #end if
64 #end for
65 #end if
66
67 #if $rep_param_charges:
68 -charges
69 #for token in $rep_param_charges:
70 #if " " in str(token):
71 "$token.param_charges"
72 #else
73 $token.param_charges
74 #end if
75 #end for
76 #end if
77 #if $param_db:
78 -db "$param_db"
79 #end if
80 #if $param_hits:
81 -hits "$param_hits"
82 #end if
83 #if $param_cleavage:
84 -cleavage
85 #if " " in str($param_cleavage):
86 "$param_cleavage"
87 #else
88 $param_cleavage
89 #end if
90 #end if
91 #if $param_missed_cleavages:
92 -missed_cleavages $param_missed_cleavages
93 #end if
94 #if $param_sig_threshold:
95 -sig_threshold $param_sig_threshold
96 #end if
97 #if $param_pep_homol:
98 -pep_homol $param_pep_homol
99 #end if
100 #if $param_pep_ident:
101 -pep_ident $param_pep_ident
102 #end if
103 #if $param_pep_rank:
104 -pep_rank $param_pep_rank
105 #end if
106 #if $param_prot_score:
107 -prot_score $param_prot_score
108 #end if
109 #if $param_pep_score:
110 -pep_score $param_pep_score
111 #end if
112 #if $param_pep_exp_z:
113 -pep_exp_z $param_pep_exp_z
114 #end if
115 #if $param_show_unassigned:
116 -show_unassigned $param_show_unassigned
117 #end if
118 #if $param_first_dim_rt:
119 -first_dim_rt $param_first_dim_rt
120 #end if
121 #if $param_boundary:
122 -boundary "$param_boundary"
123 #end if
124 #if $param_mass_type:
125 -mass_type
126 #if " " in str($param_mass_type):
127 "$param_mass_type"
128 #else
129 $param_mass_type
130 #end if
131 #end if
132 #if $param_mascot_directory:
133 -mascot_directory "$param_mascot_directory"
134 #end if
135 #if $param_temp_data_directory:
136 -temp_data_directory "$param_temp_data_directory"
137 #end if
138 #if $adv_opts.adv_opts_selector=='advanced':
139 #if $adv_opts.param_force:
140 -force
141 #end if
142 #end if
143 ]]></command>
144 <inputs> 43 <inputs>
145 <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/> 44 <param name="in" argument="-in" type="data" format="txt" optional="false" label="input file in mzData format" help="Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read select txt data sets(s)"/>
146 <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/> 45 <param name="mascot_in" argument="-mascot_in" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help=""/>
147 <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/> 46 <param name="mascot_out" argument="-mascot_out" type="boolean" truevalue="true" falsevalue="false" checked="false" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help=""/>
148 <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) "> 47 <param name="instrument" argument="-instrument" type="text" optional="true" value="Default" label="the instrument that was used to measure the spectra" help="">
149 <sanitizer> 48 <expand macro="list_string_san"/>
150 <valid initial="string.printable"> 49 </param>
151 <remove value="'"/> 50 <param name="precursor_mass_tolerance" argument="-precursor_mass_tolerance" type="float" optional="true" value="2.0" label="the precursor mass tolerance" help=""/>
152 <remove value="&quot;"/> 51 <param name="peak_mass_tolerance" argument="-peak_mass_tolerance" type="float" optional="true" value="1.0" label="the peak mass tolerance" help=""/>
153 </valid> 52 <param name="taxonomy" argument="-taxonomy" type="select" optional="false" label="the taxonomy" help="">
154 </sanitizer>
155 </param>
156 <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance) "/>
157 <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance) "/>
158 <param name="param_taxonomy" type="select" optional="False" value="All entries" label="the taxonomy" help="(-taxonomy) ">
159 <option value="All entries" selected="true">All entries</option> 53 <option value="All entries" selected="true">All entries</option>
160 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option> 54 <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
161 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option> 55 <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
162 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option> 56 <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option>
163 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option> 57 <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option>
219 <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option> 113 <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option>
220 <option value=". . . . Other viruses">. . . . Other viruses</option> 114 <option value=". . . . Other viruses">. . . . Other viruses</option>
221 <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option> 115 <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option>
222 <option value=". . unclassified">. . unclassified</option> 116 <option value=". . unclassified">. . unclassified</option>
223 <option value=". . Species information unavailable">. . Species information unavailable</option> 117 <option value=". . Species information unavailable">. . Species information unavailable</option>
224 </param> 118 <expand macro="list_string_san"/>
225 <repeat name="rep_param_modifications" min="0" title="param_modifications"> 119 </param>
226 <param name="param_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-modifications) "> 120 <param name="modifications" argument="-modifications" type="text" optional="true" value="" label="the modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
227 <sanitizer> 121 <expand macro="list_string_val"/>
228 <valid initial="string.printable"> 122 <expand macro="list_string_san"/>
229 <remove value="'"/> 123 </param>
230 <remove value="&quot;"/> 124 <param name="variable_modifications" argument="-variable_modifications" type="text" optional="true" value="" label="the variable modifications i.e. Carboxymethyl (C)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
231 </valid> 125 <expand macro="list_string_val"/>
232 </sanitizer> 126 <expand macro="list_string_san"/>
233 </param> 127 </param>
234 </repeat> 128 <param name="charges" argument="-charges" type="text" optional="true" value="1+ 2+ 3+" label="the different charge states" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
235 <repeat name="rep_param_variable_modifications" min="0" title="param_variable_modifications"> 129 <expand macro="list_string_val"/>
236 <param name="param_variable_modifications" type="text" size="30" label="the variable modifications i.e. Carboxymethyl (C)" help="(-variable_modifications) "> 130 <expand macro="list_string_san"/>
237 <sanitizer> 131 </param>
238 <valid initial="string.printable"> 132 <param name="db" argument="-db" type="text" optional="true" value="MSDB" label="the database to search in" help="">
239 <remove value="'"/> 133 <expand macro="list_string_san"/>
240 <remove value="&quot;"/> 134 </param>
241 </valid> 135 <param name="hits" argument="-hits" type="text" optional="true" value="AUTO" label="the number of hits to report" help="">
242 </sanitizer> 136 <expand macro="list_string_san"/>
243 </param> 137 </param>
244 </repeat> 138 <param name="cleavage" argument="-cleavage" type="select" optional="false" label="The enzyme descriptor to the enzyme used for digestion" help="(Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
245 <repeat name="rep_param_charges" min="0" max="1" title="param_charges">
246 <param name="param_charges" type="text" size="30" value="1+ 2+ 3+" label="the different charge states" help="(-charges) ">
247 <sanitizer>
248 <valid initial="string.printable">
249 <remove value="'"/>
250 <remove value="&quot;"/>
251 </valid>
252 </sanitizer>
253 </param>
254 </repeat>
255 <param name="param_db" type="text" size="30" value="MSDB" label="the database to search in" help="(-db) ">
256 <sanitizer>
257 <valid initial="string.printable">
258 <remove value="'"/>
259 <remove value="&quot;"/>
260 </valid>
261 </sanitizer>
262 </param>
263 <param name="param_hits" type="text" size="30" value="AUTO" label="the number of hits to report" help="(-hits) ">
264 <sanitizer>
265 <valid initial="string.printable">
266 <remove value="'"/>
267 <remove value="&quot;"/>
268 </valid>
269 </sanitizer>
270 </param>
271 <param name="param_cleavage" type="select" optional="False" value="Trypsin" label="The enzyme descriptor to the enzyme used for digestion" help="(-cleavage) (Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
272 <option value="Trypsin" selected="true">Trypsin</option> 139 <option value="Trypsin" selected="true">Trypsin</option>
273 <option value="Arg-C">Arg-C</option> 140 <option value="Arg-C">Arg-C</option>
274 <option value="Asp-N">Asp-N</option> 141 <option value="Asp-N">Asp-N</option>
275 <option value="Asp-N_ambic">Asp-N_ambic</option> 142 <option value="Asp-N_ambic">Asp-N_ambic</option>
276 <option value="Chymotrypsin">Chymotrypsin</option> 143 <option value="Chymotrypsin">Chymotrypsin</option>
286 <option value="V8-DE">V8-DE</option> 153 <option value="V8-DE">V8-DE</option>
287 <option value="V8-E">V8-E</option> 154 <option value="V8-E">V8-E</option>
288 <option value="semiTrypsin">semiTrypsin</option> 155 <option value="semiTrypsin">semiTrypsin</option>
289 <option value="LysC+AspN">LysC+AspN</option> 156 <option value="LysC+AspN">LysC+AspN</option>
290 <option value="None">None</option> 157 <option value="None">None</option>
291 </param> 158 <expand macro="list_string_san"/>
292 <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="0" label="number of allowed missed cleavages" help="(-missed_cleavages) "/> 159 </param>
293 <param name="param_sig_threshold" type="float" value="0.05" label="significance threshold" help="(-sig_threshold) "/> 160 <param name="missed_cleavages" argument="-missed_cleavages" type="integer" optional="true" min="0" value="0" label="number of allowed missed cleavages" help=""/>
294 <param name="param_pep_homol" type="float" value="1.0" label="peptide homology threshold" help="(-pep_homol) "/> 161 <param name="sig_threshold" argument="-sig_threshold" type="float" optional="true" value="0.05" label="significance threshold" help=""/>
295 <param name="param_pep_ident" type="float" value="1.0" label="peptide ident threshold" help="(-pep_ident) "/> 162 <param name="pep_homol" argument="-pep_homol" type="float" optional="true" value="1.0" label="peptide homology threshold" help=""/>
296 <param name="param_pep_rank" type="integer" value="1" label="peptide rank" help="(-pep_rank) "/> 163 <param name="pep_ident" argument="-pep_ident" type="float" optional="true" value="1.0" label="peptide ident threshold" help=""/>
297 <param name="param_prot_score" type="float" value="1.0" label="protein score" help="(-prot_score) "/> 164 <param name="pep_rank" argument="-pep_rank" type="integer" optional="true" value="1" label="peptide rank" help=""/>
298 <param name="param_pep_score" type="float" value="1.0" label="peptide score" help="(-pep_score) "/> 165 <param name="prot_score" argument="-prot_score" type="float" optional="true" value="1.0" label="protein score" help=""/>
299 <param name="param_pep_exp_z" type="integer" value="1" label="peptide expected charge" help="(-pep_exp_z) "/> 166 <param name="pep_score" argument="-pep_score" type="float" optional="true" value="1.0" label="peptide score" help=""/>
300 <param name="param_show_unassigned" type="integer" value="1" label="show_unassigned" help="(-show_unassigned) "/> 167 <param name="pep_exp_z" argument="-pep_exp_z" type="integer" optional="true" value="1" label="peptide expected charge" help=""/>
301 <param name="param_first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help="(-first_dim_rt) "/> 168 <param name="show_unassigned" argument="-show_unassigned" type="integer" optional="true" value="1" label="show_unassigned" help=""/>
302 <param name="param_boundary" type="text" size="30" label="MIME boundary for mascot output format" help="(-boundary) "> 169 <param name="first_dim_rt" argument="-first_dim_rt" type="float" optional="true" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help=""/>
303 <sanitizer> 170 <param name="boundary" argument="-boundary" type="text" optional="true" value="" label="MIME boundary for mascot output format" help="">
304 <valid initial="string.printable"> 171 <expand macro="list_string_san"/>
305 <remove value="'"/> 172 </param>
306 <remove value="&quot;"/> 173 <param name="mass_type" argument="-mass_type" display="radio" type="select" optional="false" label="mass type" help="">
307 </valid>
308 </sanitizer>
309 </param>
310 <param name="param_mass_type" display="radio" type="select" optional="False" value="Monoisotopic" label="mass type" help="(-mass_type) ">
311 <option value="Monoisotopic" selected="true">Monoisotopic</option> 174 <option value="Monoisotopic" selected="true">Monoisotopic</option>
312 <option value="Average">Average</option> 175 <option value="Average">Average</option>
313 </param> 176 <expand macro="list_string_san"/>
314 <param name="param_mascot_directory" type="text" size="30" label="the directory in which mascot is located" help="(-mascot_directory) "> 177 </param>
315 <sanitizer> 178 <expand macro="adv_opts_macro">
316 <valid initial="string.printable"> 179 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
317 <remove value="'"/> 180 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
318 <remove value="&quot;"/> 181 <expand macro="list_string_san"/>
319 </valid> 182 </param>
320 </sanitizer>
321 </param>
322 <param name="param_temp_data_directory" type="text" size="30" label="a directory in which some temporary files can be stored" help="(-temp_data_directory) ">
323 <sanitizer>
324 <valid initial="string.printable">
325 <remove value="'"/>
326 <remove value="&quot;"/>
327 </valid>
328 </sanitizer>
329 </param>
330 <expand macro="advanced_options">
331 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
332 </expand> 183 </expand>
184 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
185 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
186 </param>
333 </inputs> 187 </inputs>
334 <outputs> 188 <outputs>
335 <data name="param_out" format="data"/> 189 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
190 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
191 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
192 </data>
336 </outputs> 193 </outputs>
337 <help>Annotates MS/MS spectra using Mascot. 194 <tests>
338 195 <expand macro="autotest_MascotAdapter"/>
339 196 <expand macro="manutest_MascotAdapter"/>
340 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MascotAdapter.html</help> 197 </tests>
198 <help><![CDATA[Annotates MS/MS spectra using Mascot.
199
200
201 For more information, visit http://www.openms.de/documentation/TOPP_MascotAdapter.html]]></help>
202 <expand macro="references"/>
341 </tool> 203 </tool>