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comparison check.xml @ 0:26467f738ed4 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author chemteam
date Tue, 12 Jul 2022 12:48:09 +0000
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1 <tool id="gmx_check" name="GROMACS check" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="@PROFILE@">
2 <description>to provide information about GROMACS input files</description>
3 <macros>
4 <token name="@GALAXY_VERSION@">0</token>
5 <token name="@PROFILE@">21.05</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <command detect_errors="exit_code"><![CDATA[
10 #if $input_file.calculate_select == "info_traj":
11 ln -s '$input_file.traj_file' './traj.$input_file.traj_file.ext' &&
12 gmx check
13 -f './traj.$input_file.traj_file.ext'
14 &> '$out_info_traj'
15 #elif $input_file.calculate_select == "compare_traj":
16 ln -s '$input_file.traj_file' './traj1.$input_file.traj_file.ext' &&
17 ln -s '$input_file.traj_file2' './traj2.$input_file.traj_file2.ext' &&
18 gmx check
19 -f './traj1.$input_file.traj_file.ext'
20 -f2 './traj2.$input_file.traj_file2.ext'
21 $input_file.rmsd
22 -tol '$input_file.rel_tol'
23 -abstol '$input_file.abs_tol'
24 &> '$out_compare_traj'
25 #elif $input_file.calculate_select == "info_struc":
26 ln -s '$input_file.struc_file' './struc.$input_file.struc_file.ext' &&
27 gmx check
28 -c './struc.$input_file.struc_file.ext'
29 -vdwfac '$input_file.vdwfac'
30 -bonlo '$input_file.bonlo'
31 -bonhi '$input_file.bonhi'
32 &> '$out_info_struc'
33 #elif $input_file.calculate_select == "info_ener":
34 ln -s '$input_file.ener_file' './ener.$input_file.ener_file.ext' &&
35 gmx check
36 -e './ener.$input_file.ener_file.ext'
37 &> '$out_info_ener'
38 #elif $input_file.calculate_select == "info_ind":
39 ln -s '$input_file.ind_file' './index.$input_file.ind_file.ext' &&
40 gmx check
41 -n './index.$input_file.ind_file.ext'
42 &> '$out_info_ind'
43 #elif $input_file.calculate_select == "compare_ener":
44 ln -s '$input_file.ener_file' './ener1.$input_file.ener_file.ext' &&
45 ln -s '$input_file.ener_file2' './ener2.$input_file.ener_file2.ext' &&
46 gmx check
47 -e './ener1.$input_file.ener_file.ext'
48 -e2 './ener2.$input_file.ener_file2.ext'
49 -tol '$input_file.rel_tol'
50 -abstol '$input_file.abs_tol'
51 -lastener '$input_file.lastener'
52 &> '$out_compare_ener'
53 #else:
54 ln -s '$input_file.top_file' './top1.$input_file.top_file.ext' &&
55 ln -s '$input_file.top_file2' './top2.$input_file.top_file2.ext'&&
56 gmx check
57 -s1 './top1.$input_file.top_file.ext'
58 -s2 './top2.$input_file.top_file2.ext'
59 -abstol '$input_file.abs_tol'
60 &> '$out_compare_topol'
61 #end if
62 ]]></command>
63 <inputs>
64 <conditional name="input_file">
65 <param name="calculate_select" type="select" label="Select the type of information you want to obtain">
66 <option value="info_traj">Information about a trajectory</option>
67 <option value="compare_traj">Compare two trajectories</option>
68 <option value="info_struc">Information about the system structure</option>
69 <option value="info_ener">Information about the system energy</option>
70 <option value="info_ind">Information about the system index</option>
71 <option value="compare_top">Compare two topologies</option>
72 <option value="compare_ener">Compare two energy files</option>
73 </param>
74 <when value="info_traj">
75 <param name="traj_file" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file" help="Enter the trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/>
76 </when>
77 <when value="compare_traj">
78 <param name="traj_file" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file 1" help="Enter the first trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/>
79 <param name="traj_file2" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file 2" help="Enter the second trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/>
80 <param name="rmsd" type="boolean" truevalue="-rmsd" falsevalue="" label="Do you want to display the RMSD?"/>
81 <param name="rel_tol" type="float" max="1.0" value="0.001" label="Enter relative tolerance" help="Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)."/>
82 <param name="abs_tol" type="float" max="1.0" value="0.001" optional="True" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/>
83 </when>
84 <when value="info_struc">
85 <param name="struc_file" type="data" format="tpr, gro, pdb, brk, ent" label="Structure file" help="Enter the structure file. Accepted formats: tpr, gro, pdb, brk, ent.">
86 <validator type="expression" message="Wrong file format">value.extension != 'edr' and value.extension != 'xtc'</validator>
87 </param>
88 <param name="vdwfac" type="float" max="1.0" value="0.8" label="Enter the fraction of sum of VdW radii sum"/>
89 <param name="bonlo" type="float" max="1.0" value="0.4" label="Enter the minimal fraction of sum of van der Waals radii for bonded atoms"/>
90 <param name="bonhi" type="float" max="1.0" value="0.7" label="Enter the maximal fraction of sum of van der Waals radii for bonded atoms"/>
91 </when>
92 <when value="info_ener">
93 <param name="ener_file" type="data" format="edr" label="Energy file" help="Enter the energy file. Accepted format: edr."/>
94 </when>
95 <when value="info_ind">
96 <param name="ind_file" type="data" format="ndx" label="Index file" help="Enter the index file. Accepted format: ndx."/>
97 </when>
98 <when value="compare_top">
99 <param name="top_file" type="data" format="tpr" label="Topology file 1" help="Enter the first topology file. Accepted format: tpr.">
100 <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator>
101 </param>
102 <param name="top_file2" type="data" format="tpr" label="Topology file 2" help="Enter the second topology file. Accepted format: tpr.">
103 <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator>
104 </param>
105 <param name="abs_tol" type="float" max="1.0" value="0.001" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/>
106 </when>
107 <when value="compare_ener">
108 <param name="ener_file" type="data" format="edr" label="Energy file 1" help="Enter the first energy file. Accepted format: edr."/>
109 <param name="ener_file2" type="data" format="edr" label="Energy file 2" help="Enter the second energy file. Accepted format: edr."/>
110 <param name="rel_tol" type="float" max="1.0" value="0.001" label="Enter relative tolerance" help="Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)."/>
111 <param name="abs_tol" type="float" max="1.0" value="0.001" optional="True" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/>
112 <param name="lastener" type="text" value="all" label="Enter the last energy term to compare" help="Last energy term to compare. It makes sense to go up until the Pressure."/>
113 </when>
114 </conditional>
115 </inputs>
116 <outputs>
117 <data name="out_info_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : information on trajectory on ${on_string}">
118 <filter>input_file["calculate_select"] == "info_traj"</filter>
119 </data>
120 <data name="out_compare_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : compare trajectories on ${on_string}">
121 <filter>input_file["calculate_select"] == "compare_traj"</filter>
122 </data>
123 <data name="out_info_struc" format="txt" from_work_dir="*.txt" label="${tool.name} : information on structure on ${on_string}">
124 <filter>input_file["calculate_select"] == "info_struc"</filter>
125 </data>
126 <data name="out_info_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : information on energy on ${on_string}">
127 <filter>input_file["calculate_select"] == "info_ener"</filter>
128 </data>
129 <data name="out_info_ind" format="txt" from_work_dir="*.txt" label="${tool.name} : information on index file on ${on_string}">
130 <filter>input_file["calculate_select"] == "info_ind"</filter>
131 </data>
132 <data name="out_compare_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : compare energy files on ${on_string}">
133 <filter>input_file["calculate_select"] == "compare_ener"</filter>
134 </data>
135 <data name="out_compare_topol" format="txt" from_work_dir="*.txt" label="${tool.name} : compare topology files on ${on_string}">
136 <filter>input_file["calculate_select"] == "compare_top"</filter>
137 </data>
138 </outputs>
139 <tests>
140 <test>
141 <conditional name="input_file">
142 <param name="calculate_select" value="info_traj"/>
143 <param name="traj_file" value="nvt.xtc" ftype="xtc"/>
144 </conditional>
145 <output name="out_info_traj" file="check_info_traj.txt" ftype="txt" lines_diff="8"/>
146 </test>
147 <test>
148 <conditional name="input_file">
149 <param name="calculate_select" value="compare_traj"/>
150 <param name="traj_file" value="nvt.xtc" ftype="xtc"/>
151 <param name="traj_file2" value="npt.xtc" ftype="xtc"/>
152 <param name="rmsd" value="True"/>
153 <param name="rel_tol" value="0.1"/>
154 <param name="abs_tol" value="0.1"/>
155 </conditional>
156 <output name="out_compare_traj" file="check_compare_traj.txt" ftype="txt" lines_diff="8"/>
157 </test>
158 <test>
159 <conditional name="input_file">
160 <param name="calculate_select" value="info_struc"/>
161 <param name="struc_file" value="minim.gro" ftype="gro"/>
162 <param name="vdwfac" value="0.8"/>
163 <param name="bonlo" value="0.4"/>
164 <param name="bonhi" value="0.7"/>
165 </conditional>
166 <output name="out_info_struc" file="check_info_structure.txt" ftype="txt" lines_diff="10"/>
167 </test>
168 <test>
169 <conditional name="input_file">
170 <param name="calculate_select" value="info_ener"/>
171 <param name="ener_file" value="minim.edr" ftype="edr"/>
172 </conditional>
173 <output name="out_info_ener" file="check_info_energy.txt" ftype="txt" lines_diff="8"/>
174 </test>
175 <test>
176 <conditional name="input_file">
177 <param name="calculate_select" value="info_ind"/>
178 <param name="ind_file" value="index.ndx" ftype="ndx"/>
179 </conditional>
180 <output name="out_info_ind" file="check_info_index.txt" ftype="txt" lines_diff="8"/>
181 </test>
182 <test>
183 <conditional name="input_file">
184 <param name="calculate_select" value="compare_top"/>
185 <param name="top_file" value="npt.tpr" ftype="tpr"/>
186 <param name="top_file2" value="npt2.tpr" ftype="tpr"/>
187 <param name="abs_tol" value="0.1"/>
188 </conditional>
189 <output name="out_compare_topol" file="check_compare_topology.txt" ftype="txt" lines_diff="8"/>
190 </test>
191 <test>
192 <conditional name="input_file">
193 <param name="calculate_select" value="compare_ener"/>
194 <param name="ener_file" value="minim.edr" ftype="edr"/>
195 <param name="ener_file2" value="outp.edr" ftype="edr"/>
196 <param name="rel_tol" value="0.1"/>
197 <param name="abs_tol" value="0.1"/>
198 <param name="lastener" value="Pressure"/>
199 </conditional>
200 <output name="out_compare_ener" file="check_compare_energy.txt" ftype="txt" lines_diff="8"/>
201 </test>
202 </tests>
203 <help><![CDATA[
204
205 .. class:: infomark
206
207 **What it does**
208
209 This tool reads a trajectory (trr or xtc), an energy file (edr) or an index file (ndx) and prints out useful information about them.
210
211 Selecting 'information about the structure of a system' checks for the presence of coordinates, velocities and the box in the file, close contacts (smaller than van der Waals radii and not bound, i.e. not between minimal fraction of sum of van der Waals radii and maximal fraction of sum of van der Waals radii, all relative to the sum of the two van der Waals radii) and atoms outside the box (these can occur often and are not a problem). If velocities are present, an estimated temperature will be calculated from them.
212
213 If an index file is given, its contents will be summarized.
214
215 The program can compare two runtime input files (tpr) when both topology file 1 and topology file 2 are provided. When comparing run input files this way, the default relative tolerance is reduced to 0.000001 and the absolute tolerance set to zero to find any differences not due to minor compiler optimization differences, although you can of course still set any other tolerances through the options. Similarly a pair of trajectory files can be compared (using compare two trajectories), or a pair of energy files (using compare two energy files).
216
217 _____
218
219 .. class:: infomark
220
221 **Inputs**
222
223 **Information about a trajectory**
224 - Trajectory file : trajectory file in xtc, trr, cpt, gro or pdb format.
225
226 **Compare two trajectories**
227 - Trajectory file 1 : trajectory file in xtc, trr, cpt, gro or pdb format.
228 - Trajectory file 2 : trajectory file in xtc, trr, cpt, gro or pdb format.
229 - Do you want to display the RMSD? : print RMSD for x, v and f.
230 - Enter relative tolerance : relative tolerance for comparing real values.
231 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
232
233 **Information about the structure of a system**
234 - Structure file : structure file in tpr, gro, pdb, brk or ent format.
235 - Enter the fraction of sum of VdW radii : fraction of sum of VdW radii used as warning cutoff.
236 - Enter the minimal fraction of sum of van der Waals radii for bonded atoms : minimal fraction of sum of van der Waals radii for bonded atoms.
237 - Enter the maximal fraction of sum of van der Waals radii for bonded atoms : maximal fraction of sum of van der Waals radii for bonded atoms.
238
239 **Information about the energy of a system**
240 - Energy file : energy file in edr format.
241
242 **Information about the index of a system**
243 - Index file : index file in ndx format.
244
245 **Compare two topologies**
246 - Topology file 1 : topology file in tpr format.
247 - Topology file 2 : topology file in tpr format.
248 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
249
250 **Compare two energy files**
251 - Energy file 1 : energy file in edr format.
252 - Energy file 2 : energy file in edr format.
253 - Enter relative tolerance : relative tolerance for comparing real values.
254 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
255 - Enter the last energy term to compare : last energy term to compare (if not given all are tested). It makes sense to go up until the pressure.
256
257 _____
258
259 .. class:: infomark
260
261 **Output**
262
263 - list with one or more text files. This file contains either information about the trajectory, the structure, the index or the energy, or a comparison between two trajectories, two topologies or two energy files.
264
265 ]]></help>
266 <citations>
267 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
268 </citations>
269 </tool>