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comparison distance.xml @ 5:d540ea77b909 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
author chemteam
date Thu, 06 Feb 2020 19:43:03 -0500
parents 312f912de69d
children ffd6f8d159e1
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4:312f912de69d 5:d540ea77b909
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
8 <![CDATA[ 8 <![CDATA[
9 python '$__tool_directory__/distance.py' 9 #if $inps.inps == 'one':
10 --itraj '$trajin' 10 python '$__tool_directory__/distance_single.py'
11 --istr '$strin' 11 --isegid1 '$inps.segid1'
12 --itrajext '$trajin.ext' 12 --iresid1 '$inps.resid1'
13 --istrext '$strin.ext' 13 --iname1 '$inps.name1'
14 --isegid1 '$segid1' 14 --isegid2 '$inps.segid2'
15 --iresid1 '$resid1' 15 --iresid2 '$inps.resid2'
16 --iname1 '$name1' 16 --iname2 '$inps.name2'
17 --isegid2 '$segid2' 17 --odistance_plot '$distance_plot'
18 --iresid2 '$resid2' 18 2>&1
19 --iname2 '$name2' 19 #elif $inps.inps == 'multiple':
20 --output '$output' 20 python '$__tool_directory__/distance_multiple.py'
21 --odistance_plot '$distance_plot' 21 --list1 '$inps.list1'
22 2>&1 22 --list2 '$inps.list2'
23 #end if
24 --itraj '$trajin'
25 --istr '$strin'
26 --itrajext '$trajin.ext'
27 --istrext '$strin.ext'
28 --output '$output'
29 $header
30
23 ]]></command> 31 ]]></command>
24 <inputs> 32 <inputs>
25 <expand macro="analysis_inputs"/> 33 <expand macro="analysis_inputs"/>
26 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/> 34
27 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/> 35 <conditional name="inps">
28 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/> 36 <param argument="inps" type="select" label="Number of pairwise distances to calculate?">
29 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/> 37 <option value="one" selected="true">One</option>
30 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/> 38 <option value="multiple">Multiple</option>
31 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/> 39 </param>
40 <when value="one">
41 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
42 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
43 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
44 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
45 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
46 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
47 </when>
48 <when value="multiple">
49 <param name="list1" type="data" format="text" label="Selection groups (list 1)"/>
50 <param name="list2" type="data" format="text" label="Selection groups (list 2)"/>
51 </when>
52 </conditional>
53 <param name="header" type="boolean" truevalue="--header" falsevalue="" label="Include header in output file"/>
32 </inputs> 54 </inputs>
33 <outputs> 55 <outputs>
34 <data format="tabular" name="output" label="Distance Analysis raw data"/> 56 <data format="tabular" name="output" label="Distance Analysis raw data"/>
35 <data format="png" name="distance_plot" label="Distance Analysis Plot"/> 57 <data format="png" name="distance_plot" label="Distance Analysis Plot">
58 <filter>inps == 'one'</filter>
59 </data>
36 </outputs> 60 </outputs>
37 <tests> 61 <tests>
38 <test> 62 <test>
39 <expand macro="tests_inputs"/> 63 <expand macro="tests_inputs"/>
40 <param name="segid1" value="PRO"/> 64 <param name="segid1" value="PRO"/>
41 <param name="resid1" value="212"/> 65 <param name="resid1" value="212"/>
42 <param name="name1" value="OE2"/> 66 <param name="name1" value="OE2"/>
43 <param name="segid2" value="HET"/> 67 <param name="segid2" value="HET"/>
44 <param name="resid2" value="3"/> 68 <param name="resid2" value="3"/>
45 <param name="name2" value="C1"/> 69 <param name="name2" value="C1"/>
70 <param name="header" value="false"/>
46 <output name="output" file="Distance_Analysis_raw_data.tabular" /> 71 <output name="output" file="Distance_Analysis_raw_data.tabular" />
47 </test> 72 </test>
48 <test> 73 <test>
49 <expand macro="tests_inputs_gmx"/> 74 <expand macro="tests_inputs_gmx"/>
50 <param name="segid1" value="SYSTEM"/> 75 <param name="segid1" value="SYSTEM"/>
51 <param name="resid1" value="212"/> 76 <param name="resid1" value="212"/>
52 <param name="name1" value="OE2"/> 77 <param name="name1" value="OE2"/>
53 <param name="segid2" value="SYSTEM"/> 78 <param name="segid2" value="SYSTEM"/>
54 <param name="resid2" value="3"/> 79 <param name="resid2" value="3"/>
55 <param name="name2" value="C1"/> 80 <param name="name2" value="C1"/>
81 <param name="header" value="false"/>
56 <output name="output"> 82 <output name="output">
57 <assert_contents> 83 <assert_contents>
58 <has_n_columns n="2" /> 84 <has_n_columns n="2" />
59 <has_line_matching expression="0\s+3.8.*" /> 85 <has_line_matching expression="0\s+3.893.*" />
60 <has_line_matching expression="14\s+3.2.*" /> 86 <has_line_matching expression="14\s+3.262.*" />
87 </assert_contents>
88 </output>
89 </test>
90 <test>
91 <expand macro="tests_inputs_gmx"/>
92 <param name="inps" value="multiple"/>
93 <param name="list1" value="list1.txt"/>
94 <param name="list2" value="list2.txt"/>
95 <param name="header" value="true"/>
96 <output name="output">
97 <assert_contents>
98 <has_n_columns n="2" />
99 <has_line_matching expression="Frame\s+resid_212_and_name_OE2-resid_3_and_name_C1" />
100 <has_line_matching expression="0\s+3.893.*" />
101 <has_line_matching expression="14\s+3.262.*" />
61 </assert_contents> 102 </assert_contents>
62 </output> 103 </output>
63 </test> 104 </test>
64 </tests> 105 </tests>
65 <help><![CDATA[ 106 <help><![CDATA[
66 .. class:: infomark 107 .. class:: infomark
67 108
68 **What it does** 109 **What it does**
69 110
70 This tool calculates and plots the distance between the two atoms. 111 This tool calculates and plots the distance between pairs of atoms. Two modes are
112 available: single pair mode, where distances are calculated between two specified
113 atoms, and multiple pair mode, where two lists of atoms need to be provided.
71 114
72 _____ 115 _____
73 116
74 117
75 .. class:: infomark 118 .. class:: infomark
76 119
77 **Input** 120 **Input**
78 121
79 - Trajectory file (DCD). 122 - Trajectory file (DCD).
80 - PDB file. 123 - PDB file.
81 - Segment IDs, Residue IDs and names of two atoms to calculate distances.
82 124
83 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system. 125 In single pair mode, segment IDs, residue IDs and names of two atoms are selected.
126 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one
127 protein or all the solvent molecules or simply the whole system.
128
129 In multiple pair mode, two files need to be uploaded, each with one or more atom
130 groups defined using the MDAnalysis atom selection, each on a new line. For example:
131
132 ::
133
134 resid 163
135 resid 56
136 resid 12 and type N
137
138 All possible distances between the two sets of atom groups will be calculated. For
139 example, if List 1 contains 5 atoms and List 2 contains 8 atoms, the output file will
140 contain 40 columns, each with the distance between one group in List 1 and one group
141 in List 2.
142
143 Note that in multiple pair mode, if the group has multiple atoms, the center of mass
144 will be used for the calculation.
84 145
85 _____ 146 _____
86 147
87 148
88 .. class:: infomark 149 .. class:: infomark