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comparison ramclustr_define_experiment.xml @ 0:42c2a25ff197 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
author recetox
date Wed, 29 Jun 2022 10:00:43 +0000
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1 <tool id="ramclustr_define_experiment" name="RAMClustR define experiment" version="1.0.2">
2 <description>Definition of experimental design used for record keeping and writing spectra data.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creator"/>
7
8 <command detect_errors="exit_code"><![CDATA[
9 sh ${ramclustr_define_experiment_cli}
10 ]]>
11 </command>
12 <configfiles>
13 <configfile name="ramclustr_define_experiment_cli">
14 python3 ${__tool_directory__}/ramclustr_define_experiment_wrapper.py \
15 --Experiment "$design.Experiment" \
16 --Species "$design.Species" \
17 --Sample "$design.Sample" \
18 --Contributer "$design.Contributor" \
19 --platform "$platform.platform_choice.choice" \
20 #if $platform.platform_choice.choice == "GC-MS":
21 --chrominst "$platform.platform_choice.chrominst" \
22 --msinst "$platform.platform_choice.msinst" \
23 --column "$platform.platform_choice.column" \
24 --InletTemp "$platform.platform_choice.InletTemp" \
25 --TransferTemp "$platform.platform_choice.TransferTemp" \
26 --mstype "$platform.platform_choice.gc_mstype" \
27 --msmode "$platform.platform_choice.msmode" \
28 --ionization "$platform.platform_choice.gc_ionization" \
29 --msscanrange "$platform.platform_choice.msscanrange" \
30 --scantime "$platform.platform_choice.scantime" \
31 --deriv "$platform.platform_choice.deriv" \
32 --MSlevs "$platform.platform_choice.MSlevs" \
33 #else:
34 --chrominst "$platform.platform_choice.chrominst" \
35 --msinst "$platform.platform_choice.msinst" \
36 --column "$platform.platform_choice.column" \
37 --solvA "$platform.platform_choice.solvA" \
38 --solvB "$platform.platform_choice.solvB" \
39 --CE1 "$platform.platform_choice.CE1" \
40 --CE2 "$platform.platform_choice.CE2" \
41 --mstype "$platform.platform_choice.lc_mstype" \
42 --msmode "$platform.platform_choice.msmode" \
43 --ionization "$platform.platform_choice.lc_ionization" \
44 --colgas "$platform.platform_choice.colgas" \
45 --msscanrange "$platform.platform_choice.msscanrange" \
46 --conevol "$platform.platform_choice.conevol" \
47 --MSlevs "$platform.platform_choice.MSlevs" \
48 #end if
49 --output_file "$RAMClustR_experiment"
50 </configfile>
51 </configfiles>
52 <inputs>
53 <section name="design" title="Experimental Design" expanded="true">
54 <param name="Experiment" type="text" label="Experiment name (no spaces).">
55 <validator type="empty_field"/>
56 </param>
57 <param name="Species" type="text" label="Genus species from which samples are derived."/>
58 <param name="Sample" type="text" label="Type of sample (e.g., serum, leaf)."/>
59 <param name="Contributor" type="text" label="Your or your PI's name."/>
60 </section>
61
62 <section name="platform" title="Platform" expanded="true">
63 <conditional name="platform_choice">
64 <param name="choice" type="select" label="Choose platform:">
65 <option value="GC-MS" selected="true">GC-MS</option>
66 <option value="LC-MS">LC-MS</option>
67 </param>
68 <when value="GC-MS">
69 <param name="chrominst" type="text" label="Model of GC instrument."/>
70 <param name="msinst" type="text" label="Model of MS instrument."/>
71 <param name="column" type="text" label="Column description."/>
72 <param name="InletTemp" type="text" label="Temperature of inlet."/>
73 <param name="TransferTemp" type="text" label="Temperature of GC to MS transfer line."/>
74 <param name="gc_mstype" type="select" label="Type of mass spectrometer:">
75 <option value="QQQ" selected="true">QQQ</option>
76 <option value="TOF">TOF</option>
77 <option value="QTOF">QTOF</option>
78 <option value="Orbi">Orbi</option>
79 <option value="Q">Q</option>
80 </param>
81 <param name="msmode" type="select" label="Ion mode:">
82 <option value="positive" selected="true">positive</option>
83 <option value="negative">negative</option>
84 </param>
85 <param name="gc_ionization" type="select" label="Ionization:">
86 <option value="EI" selected="true">EI</option>
87 <option value="AP">AP</option>
88 <option value="CI">CI</option>
89 </param>
90 <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
91 <param name="scantime" type="float" value="0.2" label="Time for each full scan spectrum (e.g. 0.2 seconds)."/>
92 <param name="deriv" type="select" label="Derivitization:">
93 <option value="TMS" selected="true">TMS</option>
94 <option value="TBDMS">TBDMS</option>
95 <option value="None">None</option>
96 </param>
97 <param name="MSlevs" type="float" value="1" label="Number of levels of energy acquired - 1 typically."/>
98 </when>
99 <when value="LC-MS">
100 <param name="chrominst" type="text" label="Model of LC instrument."/>
101 <param name="msinst" type="text" label="Model of MS instrument."/>
102 <param name="column" type="text" label="Column description."/>
103 <param name="solvA" type="text" label="Solvent A composition."/>
104 <param name="solvB" type="text" label="Solvent B composition."/>
105 <param name="CE1" type="text" label="Collision energy of acquisition of MS data."/>
106 <param name="CE2" type="text" label="Collision energy of acquisition for MSe/idMSMS data (when applicable)."/>
107 <param name="lc_mstype" type="select" label="Type of mass spectrometer:">
108 <option value="QQQ" selected="true">QQQ</option>
109 <option value="TOF">TOF</option>
110 <option value="QTOF">QTOF</option>
111 <option value="Orbi">Orbi</option>
112 <option value="Q">Q</option>
113 </param>
114 <param name="msmode" type="select" label="Ion mode:">
115 <option value="positive" selected="true">positive</option>
116 <option value="negative">negative</option>
117 </param>
118 <param name="lc_ionization" type="select" label="Ionization:">
119 <option value="ESI" selected="true">ESI</option>
120 <option value="APCI">APCI</option>
121 </param>
122 <param name="colgas" type="text" label="Gas used for collisional dissociation."/>
123 <param name="msscanrange" type="text" label="Scan range used for acquisition."/>
124 <param name="conevol" type="text" label="Cone voltage used for acquisition."/>
125 <param name="MSlevs" type="float" value="1" label="number of levels of energy in XCMS object data - 1 typically."/>
126 </when>
127 </conditional>
128 </section>
129 </inputs>
130
131 <outputs>
132 <data label="RAMClustR experiment definition" name="RAMClustR_experiment" format="csv" />
133 </outputs>
134
135 <tests>
136 <test><!-- TEST 1 -->
137 <section name="design">
138 <param name="Experiment" value="experiment_gc"/>
139 <param name="Species" value="mus musculus"/>
140 <param name="Sample" value="serum"/>
141 <param name="Contributor" value="recetox"/>
142 </section>
143 <section name="platform">
144 <section name="platform_choice">
145 <param name="choice" value="GC-MS"/>
146 <param name="chrominst" value="ISQ 7000"/>
147 <param name="msinst" value="ISQ7K-VPI"/>
148 <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
149 <param name="InletTemp" value="33"/>
150 <param name="TransferTemp" value="23"/>
151 <param name="gc_mstype" value="QTOF"/>
152 <param name="msmode" value="positive"/>
153 <param name="gc_ionization" value="AP"/>
154 <param name="msscanrange" value="100"/>
155 <param name="scantime" value="0.2"/>
156 <param name="deriv" value="TMS"/>
157 <param name="MSlevs" value="1.0"/>
158 </section>
159 </section>
160 <output name="RAMClustR_experiment" file="gc-ramclustr-define-experiment.csv" ftype="csv"/>
161 </test>
162 <test><!-- TEST 2 -->
163 <section name="design">
164 <param name="Experiment" value="experiment_lc"/>
165 <param name="Species" value="mus musculus"/>
166 <param name="Sample" value="serum"/>
167 <param name="Contributor" value="recetox"/>
168 </section>
169 <section name="platform">
170 <section name="platform_choice">
171 <param name="choice" value="LC-MS"/>
172 <param name="chrominst" value="UltiMateX 3000 BioRS System"/>
173 <param name="msinst" value="FSN04-10000"/>
174 <param name="column" value="These columns enable analysis of ppm levels of amines without column priming"/>
175 <param name="solvA" value="H20"/>
176 <param name="solvB" value="CO2"/>
177 <param name="CE1" value="50"/>
178 <param name="CE2" value="100"/>
179 <param name="lc_mstype" value="Q"/>
180 <param name="msmode" value="negative"/>
181 <param name="lc_ionization" value="ESI"/>
182 <param name="colgas" value="He"/>
183 <param name="msscanrange" value="1000"/>
184 <param name="conevol" value="12"/>
185 <param name="MSlevs" value="1.0"/>
186 </section>
187 </section>
188 <output name="RAMClustR_experiment" file="lc-ramclustr-define-experiment.csv" ftype="csv"/>
189 </test>
190 </tests>
191
192 <help>
193 <![CDATA[
194 @HELP_experiment@
195 ]]>
196 </help>
197
198 <expand macro="citations" />
199 </tool>