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comparison HR2.xml @ 3:78afd7f439f3 draft default tip

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master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author fgiacomoni
date Wed, 15 Feb 2023 15:57:49 +0000
parents 23970530a518
children
comparison
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2:23970530a518 3:78afd7f439f3
1 <tool id="hr2" name="HR2 formula" version="1.1.3"> 1 <tool id="hr2" name="HR2 formula" version="1.2.0">
2 <description> 2 <description>
3 find a chemical formula from a accurate mass 3 find a chemical formula from a accurate mass
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.161">perl-data-dumper</requirement> 6 <requirement type="package" version="2.161">perl-data-dumper</requirement>
32 #else: 32 #else:
33 -charge "${mode_condition.qtCharge}" 33 -charge "${mode_condition.qtCharge}"
34 #end if 34 #end if
35 35
36 -regleOr "$regleOr" -atomes_basic "$atomes_basic" -atomes_sup "$atomes_sup" 36 -regleOr "$regleOr" -atomes_basic "$atomes_basic" -atomes_sup "$atomes_sup"
37
38 #if str($max_custom_atom_condition.max_custom_atom_choice) == "YES":
39 -C12_max_value "${max_custom_atom_condition.C12_max_value}"
40 -C13_max_value "${max_custom_atom_condition.C13_max_value}"
41 -H_max_value "${max_custom_atom_condition.H_max_value}"
42 -N_max_value "${max_custom_atom_condition.N_max_value}"
43 -O_max_value "${max_custom_atom_condition.O_max_value}"
44 -P_max_value "${max_custom_atom_condition.P_max_value}"
45 -S_max_value "${max_custom_atom_condition.S_max_value}"
46 -F_max_value "${max_custom_atom_condition.F_max_value}"
47 -Cl_max_value "${max_custom_atom_condition.Cl_max_value}"
48 -K_max_value "${max_custom_atom_condition.K_max_value}"
49 -Br_max_value "${max_custom_atom_condition.Br_max_value}"
50 -Na_max_value "${max_custom_atom_condition.Na_max_value}"
51
52 #end if
53
37 -output1 "$variableMetadata" -outputView "$hr2ResView" 54 -output1 "$variableMetadata" -outputView "$hr2ResView"
38 -verbose "$verbose" 55 -verbose "$verbose"
39 ]]></command> 56 ]]></command>
57 <!-- -customAtomValues "-C 0-${max_custom_atom_condition.C12_max_value} -1 0-${max_custom_atom_condition.C13_max_value} -H 0-${max_custom_atom_condition.H_max_value} -N 0-${max_custom_atom_condition.N_max_value} -O 0-${max_custom_atom_condition.O_max_value} -P 0-${max_custom_atom_condition.P_max_value} -S 0-${max_custom_atom_condition.S_max_value} -F 0-${max_custom_atom_condition.F_max_value} -L 0-${max_custom_atom_condition.Cl_max_value} -K 0-${max_custom_atom_condition.K_max_value} -B 0-${max_custom_atom_condition.Br_max_value} -A 0-${max_custom_atom_condition.Na_max_value}" -->
40 58
41 <inputs> 59 <inputs>
42 <conditional name="input_type"> 60 <conditional name="input_type">
43 <param name="choice" type="select" display="radio" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually"> 61 <param name="choice" type="select" display="radio" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually">
44 <option value="YES">YES</option> 62 <option value="YES">YES</option>
102 <option value="K">K</option> 120 <option value="K">K</option>
103 <option value="B">Br</option> 121 <option value="B">Br</option>
104 <option value="A">Na</option> 122 <option value="A">Na</option>
105 <option value="1">13C</option> 123 <option value="1">13C</option>
106 </param> 124 </param>
125 <conditional name="max_custom_atom_condition">
126 <param name="max_custom_atom_choice" label="Do you want to manage custom maximum number atoms?" type="select" display="radio" help="To work only with [13]C isotopes for example, use YES - ()Don't forget to select wanted atoms below)">
127 <option value="NO" selected="true">NO</option>
128 <option value="YES">YES</option>
129 </param>
130 <when value="YES">
131 <param name="C12_max_value" label="[12]C atom max number " type="integer" value="0" min="0" max="100" help="The maximum of [12]C you need to (should be between 0 and 100 atoms per structure). Default value is 0"/>
132 <param name="C13_max_value" label="[13]C atom max number " type="integer" value="40" min="0" max="100" help="The maximum of [13]C you need to (should be between 0 and 100 atoms per structure). Default value is 40"/>
133 <param name="H_max_value" label="[1]H atom max number " type="integer" value="200" min="0" max="200" help="The maximum of H you need to (should be between 0 and 200 atoms per structure). Default value is 200"/>
134 <param name="N_max_value" label="[15]N atom max number " type="integer" value="40" min="0" max="100" help="The maximum of N you need to (should be between 0 and 100 atoms per structure). Default value is 40"/>
135 <param name="O_max_value" label="[16]O atom max number " type="integer" value="70" min="0" max="100" help="The maximum of O you need to (should be between 0 and 100 atoms per structure). Default value is 70"/>
136 <param name="P_max_value" label="[31]P atom max number " type="integer" value="10" min="0" max="100" help="The maximum of P you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
137 <param name="S_max_value" label="[32]S atom max number " type="integer" value="10" min="0" max="100" help="The maximum of S you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
138 <param name="F_max_value" label="[19]F atom max number " type="integer" value="10" min="0" max="100" help="The maximum of F you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
139 <param name="Cl_max_value" label="[35]Cl atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Cl you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
140 <param name="K_max_value" label="[13]K atom max number " type="integer" value="10" min="0" max="100" help="The maximum of K you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
141 <param name="Br_max_value" label="[80]Br atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Br you need to (should be between 0 and 100 atoms per structure). Default value is 10"/>
142 <param name="Na_max_value" label="[23]Na atom max number " type="integer" value="10" min="0" max="100" help="The maximum of Na you need to (should be between 0 and 40 atoms per structure). Default value is 10"/>
143 </when>
144 <when value="NO">
145 </when>
146 </conditional>
107 <param name="verbose" type="select" label="Verbose level" display="radio" help=""> 147 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
108 <option value="1" selected="true">Low</option> 148 <option value="1" selected="true">Low</option>
109 <option value="3" >High</option> 149 <option value="3" >High</option>
110 </param> 150 </param>
111 </inputs> 151 </inputs>
116 156
117 <tests> 157 <tests>
118 <test> 158 <test>
119 <param name="choice" value="NO"/> 159 <param name="choice" value="NO"/>
120 <param name="masse" value="175.125"/> 160 <param name="masse" value="175.125"/>
121 <param name="tolerance" value="1.0"/> 161 <param name="tol" value="1.0"/>
122 <param name="mode" value="negative"/> 162 <param name="mode" value="negative"/>
123 <param name="qtCharge" value="1"/> 163 <param name="qtCharge" value="1"/>
124 <param name="atomes_basic" value="C,O,N,H"/> 164 <param name="atomes_basic" value="C,O,N,H"/>
125 <param name="regleOr" value="NO"/> 165 <param name="regleOr" value="NO"/>
126 <param name="verbose" value="3"/> 166 <param name="verbose" value="3"/>
127 <output name="variableMetadata" file="out1.tabular"/> 167 <output name="variableMetadata" file="out1.tabular"/>
128 </test> 168 </test>
129 <test> 169 <test>
130 <param name="choice" value="NO"/> 170 <param name="choice" value="NO"/>
131 <param name="masse" value="88.052"/> 171 <param name="masse" value="88.052"/>
132 <param name="tolerance" value="1.0"/> 172 <param name="tol" value="1.0"/>
133 <param name="mode" value="neutral"/> 173 <param name="mode" value="neutral"/>
134 <param name="qtCharge" value="1"/> 174 <param name="qtCharge" value="1"/>
135 <param name="atomes_basic" value="C,O,H"/> 175 <param name="atomes_basic" value="C,O,H"/>
136 <param name="regleOr" value="NO"/> 176 <param name="regleOr" value="NO"/>
137 <param name="verbose" value="3"/> 177 <param name="verbose" value="3"/>
138 <output name="variableMetadata" file="out2.tabular"/> 178 <output name="variableMetadata" file="out2.tabular"/>
139 </test> 179 </test>
140 <test> 180 <test>
141 <param name="choice" value="NO"/> 181 <param name="choice" value="NO"/>
142 <param name="masse" value="427.019898895"/> 182 <param name="masse" value="427.019898895"/>
143 <param name="tolerance" value="1.0"/> 183 <param name="tol" value="1.0"/>
144 <param name="mode" value="neutral"/> 184 <param name="mode" value="neutral"/>
145 <param name="qtCharge" value="1"/> 185 <param name="qtCharge" value="1"/>
146 <param name="atomes_basic" value="C,O,N,H,P"/> 186 <param name="atomes_basic" value="C,O,N,H,P"/>
147 <param name="atomes_sup" value="S"/> 187 <param name="atomes_sup" value="S"/>
188 <param name="S_max_value" value="40"/>
148 <param name="regleOr" value="NO"/> 189 <param name="regleOr" value="NO"/>
149 <param name="verbose" value="3"/> 190 <param name="verbose" value="3"/>
150 <output name="variableMetadata" file="out3.tabular"/> 191 <output name="variableMetadata" file="out3.tabular"/>
151 </test> 192 </test>
152 </tests> 193 </tests>