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comparison trj.xml @ 5:cdf93d057569 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
author chemteam
date Tue, 20 Oct 2020 10:38:49 +0000
parents 9363254ef848
children 6dcfdac2dcae
comparison
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4:9363254ef848 5:cdf93d057569
1 <tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>using trjconv and trjcat</description> 2 <description>using trjconv and trjcat</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">1</token>
6 <xml name="fit_when" token_option="none">
7 <when value="@OPTION@">
8 <param name="index_fit" type="text" label="Index of group to use for fitting" help="Index of group to use for fitting - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
9 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
10 </param>
11 </when>
12 </xml>
6 </macros> 13 </macros>
7 14
8 <expand macro="requirements" /> 15 <expand macro="requirements" />
9 16
10 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
11
12 #if $trj.trj_op == 'trjcat': 18 #if $trj.trj_op == 'trjcat':
13 mkdir trajs && 19 mkdir trajs &&
14 #for $value, $file in enumerate($trj_input): 20 #for $value, $file in enumerate($trj_input):
15 ln -s '$file' trajs/traj_${value}.${file.ext} && 21 ln -s '$file' trajs/traj_${value}.${file.ext} &&
16 #end for 22 #end for
22 28
23 #elif $trj.trj_op == 'trjconv': 29 #elif $trj.trj_op == 'trjconv':
24 ln -s '$ndx_input' ./index.ndx && 30 ln -s '$ndx_input' ./index.ndx &&
25 ln -s '$str_input' ./str.${str_input.ext} && 31 ln -s '$str_input' ./str.${str_input.ext} &&
26 ln -s '$trj_input' ./traj.${trj_input.ext} && 32 ln -s '$trj_input' ./traj.${trj_input.ext} &&
27 #if $trj.center: 33
28 echo '$trj.index_center $trj.index_output' | gmx trjconv 34 echo ## optionally pipe in the following
29 #else 35 #if $trj.fit.fit != 'none':
30 echo '$trj.index_output' | gmx trjconv 36 '$trj.fit.index_fit'
31 #end if 37 #end if
32 -f ./traj.${trj_input.ext} 38 #if $trj.pbc.pbc == 'cluster':
33 -s ./str.${str_input.ext} 39 '$trj.pbc.index_cluster'
40 #end if
41 '$trj.index_center' '$trj.index_output' | gmx trjconv
42 -f ./traj.${trj_input.ext}
43 -s ./str.${str_input.ext}
44 #if $ndx_input:
34 -n ./index.ndx 45 -n ./index.ndx
35 $trj.center 46 #end if
36 -pbc $trj.pbc 47 #if $trj.index_center:
37 -ur $trj.ur 48 -center
38 -boxcenter $trj.boxcenter 49 #end if
39 #if $time.e != -1: 50 #if $trj.sep:
40 -e '$time.e' 51 -sep
41 #end if 52 -nzero 9 ## hopefully the traj has < 1 bn frames, or collection order will be wrong
42 53 #end if
54 -pbc $trj.pbc.pbc
55 -ur $trj.ur
56 -boxcenter $trj.boxcenter
57 -fit $trj.fit.fit
58 #if $time.e != -1:
59 -e '$time.e'
60 #end if
43 #end if 61 #end if
44 62
45 -b '$time.b' 63 -b '$time.b'
46 -dt '$time.dt' 64 -dt '$time.dt'
47 -o ./output.${output_format} && 65 -o ./output.${output_format} &&
48 &>> verbose.txt && 66 &>> verbose.txt
49 mv ./output.${output_format} '$output' 67 #if not $trj.sep:
50 68 &&
69 mv ./output.${output_format} '$output'
70 #end if
51 ]]></command> 71 ]]></command>
52 72
53 <inputs> 73 <inputs>
54 <conditional name="trj"> 74 <conditional name="trj">
55 <param name="trj_op" type="select" label="Modify a trajectory or concatenate multiple trajectories?"> 75 <param name="trj_op" type="select" label="Modify a trajectory or concatenate multiple trajectories?">
56 <option value="trjconv">Modify (trjconv)</option> 76 <option value="trjconv">Modify (trjconv)</option>
57 <option value="trjcat">Concatenate (trjcat)</option> 77 <option value="trjcat">Concatenate (trjcat)</option>
58 </param> 78 </param>
59 <when value="trjconv"> 79 <when value="trjconv">
60 <param name="trj_input" type="data" format='xtc,trr' label="Input trajectory" help="In XTC or TRR format."/> 80 <param name="trj_input" type="data" format='xtc,trr,pdb,gro' label="Input trajectory" help="In XTC or TRR format; structure files with PDB or GRO format can also be used."/>
61 <param name="str_input" type="data" format='pdb,gro,tpr' label="Input structure" help="In PDB, GRO or TPR format."/> 81 <param name="str_input" type="data" format='pdb,gro,tpr' label="Input structure" help="In PDB, GRO or TPR format."/>
62 <param name="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="In NDX format."/> 82 <param name="ndx_input" type="data" format='ndx' label="Index (NDX) file" optional="true" help="In NDX format. Optional."/>
63 <param name="index_output" type="text" label="Index of group to save in the output" help="Index of group to save in the output - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)."> 83 <param name="index_output" value="0" type="text" label="Index of group to save in the output" help="Index of group to save in the output - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
64 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator> 84 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
65 </param> 85 </param>
66 <param name="center" type="boolean" label="Center system in box" truevalue="-center" falsevalue=""/>
67 <param name="index_center" type="text" label="Index of group for centering" optional="true" help="Index of group for centering - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0). Leave blank if centering is not required."> 86 <param name="index_center" type="text" label="Index of group for centering" optional="true" help="Index of group for centering - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0). Leave blank if centering is not required.">
68 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator> 87 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
69 </param> 88 </param>
70 <param name="pbc" type="select" label="PBC treatment" > 89 <param name="sep" type="select" label="Write each trajectory frame to a separate GRO or PDB file?" help="Results will be stored as a Galaxy collection. Only has effect with PDB or GRO output, otherwise ignored">
71 <option value="none">none</option> 90 <option value="" selected="true">No</option>
72 <option value="mol">mol</option> 91 <option value="sep">Yes, write each frame separately</option>
73 <option value="res">res</option> 92 </param>
74 <option value="atom">atom</option> 93 <conditional name="pbc">
75 <option value="nojump">nojump</option> 94 <param name="pbc" type="select" label="PBC treatment" >
76 <option value="cluster">cluster</option> 95 <option value="none">none</option>
77 <option value="whole">whole</option> 96 <option value="mol">mol</option>
78 </param> 97 <option value="res">res</option>
79 <param name="ur" type="select" label="Unit cell representation" > 98 <option value="atom">atom</option>
80 <option value="rect">rect</option> 99 <option value="nojump">nojump</option>
100 <option value="cluster">cluster</option>
101 <option value="whole">whole</option>
102 </param>
103 <when value="cluster">
104 <param name="index_cluster" type="text" label="Index of group to use for clustering" help="Index of group to use for clustering - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
105 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
106 </param>
107 </when>
108 <when value="none" />
109 <when value="mol" />
110 <when value="res" />
111 <when value="atom" />
112 <when value="nojump" />
113 <when value="whole" />
114 </conditional>
115 <param name="ur" type="select" label="Unit cell representation" help="Only has effect in combination with PBC treatment of mol, res or atom">
116 <option value="rect" selected="true">rect</option>
81 <option value="tric">tric</option> 117 <option value="tric">tric</option>
82 <option value="compact">compact</option> 118 <option value="compact">compact</option>
83 </param> 119 </param>
84 <param name="boxcenter" type="select" label="Center for PBC and centering treatment" > 120 <param name="boxcenter" type="select" label="Center for PBC and centering treatment" >
85 <option value="rect">rect</option> 121 <option value="rect">rect</option>
86 <option value="tric" selected="true">tric</option> 122 <option value="tric" selected="true">tric</option>
87 <option value="zero">zero</option> 123 <option value="zero">zero</option>
88 </param> 124 </param>
125 <conditional name="fit">
126 <param name="fit" type="select" label="Fit molecule to reference structure in the reference file?" >
127 <option value="none" selected="true">No fitting</option>
128 <option value="rot+trans">rot+trans</option>
129 <option value="rotxy+transxy">rotxy+transxy</option>
130 <option value="translation">translation</option>
131 <option value="transxy">transxy</option>
132 <option value="progressive">progressive</option>
133 </param>
134 <when value="none"/>
135 <expand macro="fit_when" option="rot+trans"/>
136 <expand macro="fit_when" option="rotxy+transxy"/>
137 <expand macro="fit_when" option="translation"/>
138 <expand macro="fit_when" option="transxy"/>
139 <expand macro="fit_when" option="progressive"/>
140 </conditional>
89 </when> 141 </when>
90 <when value="trjcat"> 142 <when value="trjcat">
91 <param name="trj_input" type="data" format='xtc,trr' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note this tool does not currently take order into account when concatenating." multiple="true"/> 143 <param name="trj_input" type="data" format='xtc,trr' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note this tool does not currently take order into account when concatenating." multiple="true"/>
92 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/> 144 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/>
145 <param name="sep" type="hidden" value="" />
93 </when> 146 </when>
94 </conditional> 147 </conditional>
95 <param name="output_format" type="select" label="Output format" > 148 <param name="output_format" type="select" label="Output format" >
96 <option value="xtc">XTC</option> 149 <option value="xtc">XTC</option>
97 <option value="trr">TRR</option> 150 <option value="trr">TRR</option>
105 </section> 158 </section>
106 <expand macro="log" /> 159 <expand macro="log" />
107 </inputs> 160 </inputs>
108 <outputs> 161 <outputs>
109 <data name="output" format="xtc"> 162 <data name="output" format="xtc">
163 <filter>not trj.get("sep") or output_format in ["xtc", "trr"]</filter>
110 <change_format> 164 <change_format>
111 <when input="output_format" value="trr" format="trr"/> 165 <when input="output_format" value="trr" format="trr"/>
112 <when input="output_format" value="xtc" format="xtc"/> 166 <when input="output_format" value="xtc" format="xtc"/>
113 <when input="output_format" value="gro" format="gro"/> 167 <when input="output_format" value="gro" format="gro"/>
114 <when input="output_format" value="pdb" format="pdb"/> 168 <when input="output_format" value="pdb" format="pdb"/>
115 </change_format> 169 </change_format>
116 </data> 170 </data>
117 </outputs> 171 <collection type="list" name="gro_frames" label="Trajectory frames">
172 <filter>trj.get("sep") and output_format == "gro"</filter>
173 <discover_datasets pattern="(?P&lt;designation&gt;^output[0-9]{9}\.gro$)" ext="gro"/>
174 </collection>
175 <collection type="list" name="pdb_frames" label="Trajectory frames">
176 <filter>trj.get("sep") and output_format == 'pdb'</filter>
177 <discover_datasets pattern="(?P&lt;designation&gt;^output[0-9]{9}\.pdb$)" ext="pdb"/>
178 </collection>
179 <expand macro="log_outputs" />
180 </outputs>
118 <tests> 181 <tests>
119 <test> 182 <test>
120 <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc --> 183 <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc -->
121 <param name="trj_op" value="trjcat" /> 184 <param name="trj_op" value="trjcat" />
122 <param name="trj_input" value="npt.xtc,nvt.xtc" /> 185 <param name="trj_input" value="npt.xtc,nvt.xtc" />
124 <param name="e" value="-1" /> 187 <param name="e" value="-1" />
125 <param name="dt" value="0" /> 188 <param name="dt" value="0" />
126 <param name="cat" value="true" /> 189 <param name="cat" value="true" />
127 <output name="output" file="trjcat.xtc" ftype="xtc"/> 190 <output name="output" file="trjcat.xtc" ftype="xtc"/>
128 </test> 191 </test>
129 <!-- <test> --> 192 <test>
130 <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc --> 193 <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc -->
131 <!-- <param name="trj_op" value="trjconv" /> 194 <!-- <param name="trj_op" value="trjconv" /> -->
132 <param name="trj_input" value="npt.xtc" /> 195 <param name="trj_input" value="npt.xtc" />
133 <param name="str_input" value="npt.tpr" ftype="tpr"/> 196 <param name="str_input" value="npt.tpr" ftype="tpr"/>
134 <param name="ndx_input" value="index.ndx" /> 197 <param name="ndx_input" value="index.ndx" />
135 <param name="b" value="0" /> 198 <param name="b" value="0" />
136 <param name="e" value="-1" /> 199 <param name="e" value="-1" />
137 <param name="dt" value="0" /> 200 <param name="dt" value="0" />
138 <param name="index_output" value="1" /> 201 <param name="index_output" value="1" />
139 <param name="index_center" value="1" /> 202 <param name="index_center" value="1" />
140 <param name="center" value="true" />
141 <param name="pbc" value="mol" /> 203 <param name="pbc" value="mol" />
142 <param name="ur" value="compact" />
143 <param name="ur" value="tric" /> 204 <param name="ur" value="tric" />
144 <output name="output" file="trjconv.xtc" ftype="xtc"/> 205 <output name="output" file="trjconv.xtc" ftype="xtc"/>
145 </test> --> 206 </test>
207 <test>
208 <!-- test sep flag -->
209 <param name="trj_input" value="npt.xtc" />
210 <param name="str_input" value="npt.tpr" ftype="tpr"/>
211 <param name="ndx_input" value="index.ndx" />
212 <param name="b" value="0" />
213 <param name="e" value="-1" />
214 <param name="dt" value="0" />
215 <param name="index_output" value="0" />
216 <param name="sep" value="sep" />
217 <param name="output_format" value="pdb" />
218 <output_collection name="pdb_frames" type="list">
219 <element name="output00000007" ftype="pdb" file="frame7.pdb"/>
220 </output_collection>
221 </test>
146 </tests> 222 </tests>
147 <help><![CDATA[ 223 <help><![CDATA[
148 224
149 .. class:: infomark 225 .. class:: infomark
150 226