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comparison InspectAdapter.xml @ 0:4fba18bcca36 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:17:24 -0500
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children 15ebe1509e0d
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-1:000000000000 0:4fba18bcca36
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 CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="InspectAdapter" name="InspectAdapter" version="2.1.0">
5 <description>Annotates MS/MS spectra using Inspect.</description>
6 <macros>
7 <token name="@EXECUTABLE@">InspectAdapter</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>InspectAdapter
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_out:
19 -out $param_out
20 #end if
21 #if $param_inspect_in:
22 -inspect_in
23 #end if
24 #if $param_inspect_out:
25 -inspect_out
26 #end if
27 #if $param_inspect_directory:
28 -inspect_directory "$param_inspect_directory"
29 #end if
30 #if $param_temp_data_directory:
31 -temp_data_directory "$param_temp_data_directory"
32 #end if
33 #if $param_dbs:
34 -dbs "$param_dbs"
35 #end if
36 #if $param_trie_dbs:
37 -trie_dbs "$param_trie_dbs"
38 #end if
39 #if $param_new_db:
40 -new_db "$param_new_db"
41 #end if
42 #if $param_instrument:
43 -instrument
44 #if " " in str($param_instrument):
45 "$param_instrument"
46 #else
47 $param_instrument
48 #end if
49 #end if
50 #if $param_precursor_mass_tolerance:
51 -precursor_mass_tolerance $param_precursor_mass_tolerance
52 #end if
53 #if $param_peak_mass_tolerance:
54 -peak_mass_tolerance $param_peak_mass_tolerance
55 #end if
56 #if $param_list_modifications:
57 -list_modifications
58 #end if
59 #if $param_modifications:
60 -modifications "$param_modifications"
61 #end if
62 #if $param_use_monoisotopic_mod_mass:
63 -use_monoisotopic_mod_mass
64 #end if
65 #if $param_modifications_xml_file:
66 -modifications_xml_file "$param_modifications_xml_file"
67 #end if
68 #if $param_cleavage:
69 -cleavage "$param_cleavage"
70 #end if
71 #if $param_inspect_output:
72 -inspect_output $param_inspect_output
73 #end if
74 #if $param_inspect_input:
75 -inspect_input $param_inspect_input
76 #end if
77 #if $param_multicharge:
78 -multicharge
79 #end if
80 #if $param_max_modifications_pp:
81 -max_modifications_pp $param_max_modifications_pp
82 #end if
83 #if $param_tag_count:
84 -tag_count $param_tag_count
85 #end if
86 #if $param_no_tmp_dbs:
87 -no_tmp_dbs
88 #end if
89 #if $param_p_value:
90 -p_value $param_p_value
91 #end if
92 #if $param_contact_name:
93 -contact_name "$param_contact_name"
94 #end if
95 #if $param_contact_institution:
96 -contact_institution "$param_contact_institution"
97 #end if
98 #if $param_contact_info:
99 -contact_info "$param_contact_info"
100 #end if
101 #if $param_blind_blind:
102 -blind:blind
103 #end if
104 #if $param_blind_blind_only:
105 -blind:blind_only
106 #end if
107 #if $param_blind_p_value_blind:
108 -blind:p_value_blind $param_blind_p_value_blind
109 #end if
110 #if $param_blind_snd_db:
111 -blind:snd_db "$param_blind_snd_db"
112 #end if
113 #if $param_blind_max_ptm_size:
114 -blind:max_ptm_size $param_blind_max_ptm_size
115 #end if
116 #if $adv_opts.adv_opts_selector=='advanced':
117 #if $adv_opts.param_force:
118 -force
119 #end if
120 #end if
121 </command>
122 <inputs>
123 <param name="param_in" type="data" format="mzxml" optional="False" label="input file in mzXML or mzData format" help="(-in) &lt;br&gt;Note: In mode 'inspect_out' an Inspect results file is read"/>
124 <param name="param_inspect_in" display="radio" type="boolean" truevalue="-inspect_in" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML, &lt;br&gt;write an Inspect input file and generate a trie database" help="(-inspect_in) "/>
125 <param name="param_inspect_out" display="radio" type="boolean" truevalue="-inspect_out" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file &lt;br&gt;and write idXML" help="(-inspect_out) "/>
126 <param name="param_inspect_directory" type="text" size="30" label="the directory in which Inspect is located" help="(-inspect_directory) ">
127 <sanitizer>
128 <valid initial="string.printable">
129 <remove value="'"/>
130 <remove value="&quot;"/>
131 </valid>
132 </sanitizer>
133 </param>
134 <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) ">
135 <sanitizer>
136 <valid initial="string.printable">
137 <remove value="'"/>
138 <remove value="&quot;"/>
139 </valid>
140 </sanitizer>
141 </param>
142 <param name="param_dbs" type="text" size="30" label="name(s) of database(s) to search in (FASTA and SwissProt supported)" help="(-dbs) ">
143 <sanitizer>
144 <valid initial="string.printable">
145 <remove value="'"/>
146 <remove value="&quot;"/>
147 </valid>
148 </sanitizer>
149 </param>
150 <param name="param_trie_dbs" type="text" size="30" label="name(s) of databases(s) to search in (trie-format)" help="(-trie_dbs) ">
151 <sanitizer>
152 <valid initial="string.printable">
153 <remove value="'"/>
154 <remove value="&quot;"/>
155 </valid>
156 </sanitizer>
157 </param>
158 <param name="param_new_db" type="text" size="30" label="name of the merged trie database" help="(-new_db) ">
159 <sanitizer>
160 <valid initial="string.printable">
161 <remove value="'"/>
162 <remove value="&quot;"/>
163 </valid>
164 </sanitizer>
165 </param>
166 <param name="param_instrument" display="radio" type="select" optional="True" label="the instrument that was used to measure the spectra &lt;br&gt;(If set to QTOF, uses a QTOF-derived fragmentation model, &lt;br&gt;and does not attempt to correct the parent mass.)" help="(-instrument) ">
167 <option value="ESI-ION-TRAP">ESI-ION-TRAP</option>
168 <option value="QTOF">QTOF</option>
169 <option value="FT-Hybrid">FT-Hybrid</option>
170 </param>
171 <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance) "/>
172 <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance) "/>
173 <param name="param_list_modifications" display="radio" type="boolean" truevalue="-list_modifications" falsevalue="" checked="false" optional="True" label="show a list of the available modifications" help="(-list_modifications) "/>
174 <param name="param_modifications" type="text" size="30" label="the colon-separated modifications; may be &lt;br&gt;&lt;name&gt;,&lt;type&gt;," help="(-modifications) e.g.: Deamidation,opt or &lt;br&gt;&lt;composition&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: H2C2O,KCS,opt,Acetyl or &lt;br&gt;&lt;mass&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: 42.0367,KCS,opt,Acetyl or &lt;br&gt;Valid values for type are &quot;fix&quot; and &quot;opt&quot; (default) &lt;br&gt;If you want terminal PTMs, write &quot;cterm&quot; or &quot;nterm&quot; instead of residues">
175 <sanitizer>
176 <valid initial="string.printable">
177 <remove value="'"/>
178 <remove value="&quot;"/>
179 </valid>
180 </sanitizer>
181 </param>
182 <param name="param_use_monoisotopic_mod_mass" display="radio" type="boolean" truevalue="-use_monoisotopic_mod_mass" falsevalue="" checked="false" optional="True" label="use monoisotopic masses for the modifications" help="(-use_monoisotopic_mod_mass) "/>
183 <param name="param_modifications_xml_file" type="text" size="30" label="name of an XML file with the modifications" help="(-modifications_xml_file) ">
184 <sanitizer>
185 <valid initial="string.printable">
186 <remove value="'"/>
187 <remove value="&quot;"/>
188 </valid>
189 </sanitizer>
190 </param>
191 <param name="param_cleavage" type="text" size="30" value="Trypsin" label="the enzyme used for digestion" help="(-cleavage) ">
192 <sanitizer>
193 <valid initial="string.printable">
194 <remove value="'"/>
195 <remove value="&quot;"/>
196 </valid>
197 </sanitizer>
198 </param>
199 <param name="param_inspect_input" type="data" format="text" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/>
200 <param name="param_multicharge" display="radio" type="boolean" truevalue="-multicharge" falsevalue="" checked="false" optional="True" label="attempt to guess the precursor charge and mass, &lt;br&gt;and consider multiple charge states if feasible" help="(-multicharge) "/>
201 <param name="param_max_modifications_pp" type="integer" value="-1" label="number of PTMs permitted in a single peptide" help="(-max_modifications_pp) "/>
202 <param name="param_tag_count" type="integer" value="-1" label="number of tags to generate" help="(-tag_count) "/>
203 <param name="param_no_tmp_dbs" display="radio" type="boolean" truevalue="-no_tmp_dbs" falsevalue="" checked="false" optional="True" label="no temporary databases are used" help="(-no_tmp_dbs) "/>
204 <param name="param_p_value" type="float" value="1.0" label="annotations with inferior p-value are ignored" help="(-p_value) "/>
205 <param name="param_contact_name" type="text" size="30" value="unknown" label="Name of the contact" help="(-contact_name) ">
206 <sanitizer>
207 <valid initial="string.printable">
208 <remove value="'"/>
209 <remove value="&quot;"/>
210 </valid>
211 </sanitizer>
212 </param>
213 <param name="param_contact_institution" type="text" size="30" value="unknown" label="Name of the contact institution" help="(-contact_institution) ">
214 <sanitizer>
215 <valid initial="string.printable">
216 <remove value="'"/>
217 <remove value="&quot;"/>
218 </valid>
219 </sanitizer>
220 </param>
221 <param name="param_contact_info" type="text" size="30" value="unknown" label="Some information about the contact" help="(-contact_info) ">
222 <sanitizer>
223 <valid initial="string.printable">
224 <remove value="'"/>
225 <remove value="&quot;"/>
226 </valid>
227 </sanitizer>
228 </param>
229 <param name="param_blind_blind" display="radio" type="boolean" truevalue="-blind:blind" falsevalue="" checked="false" optional="True" label="perform a blind search (allowing arbitrary modification masses), &lt;br&gt;is preceeded by a normal search to gain a smaller database" help="(-blind) &lt;br&gt;(in full mode only)"/>
230 <param name="param_blind_blind_only" display="radio" type="boolean" truevalue="-blind:blind_only" falsevalue="" checked="false" optional="True" label="like blind but no prior search is performed to reduce the database size" help="(-blind_only) "/>
231 <param name="param_blind_p_value_blind" type="float" value="1.0" label="used for generating the minimized database" help="(-p_value_blind) "/>
232 <param name="param_blind_snd_db" type="text" size="30" label="name of the minimized trie database generated when using blind mode" help="(-snd_db) ">
233 <sanitizer>
234 <valid initial="string.printable">
235 <remove value="'"/>
236 <remove value="&quot;"/>
237 </valid>
238 </sanitizer>
239 </param>
240 <param name="param_blind_max_ptm_size" type="float" value="250.0" label="maximum modification size (in Da) to conside" help="(-max_ptm_size) "/>
241 <expand macro="advanced_options">
242 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
243 </expand>
244 </inputs>
245 <outputs>
246 <data name="param_out" format="idxml"/>
247 <data name="param_inspect_output" format="data"/>
248 </outputs>
249 <help>Annotates MS/MS spectra using Inspect.
250
251
252 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InspectAdapter.html</help>
253 </tool>