Mercurial > repos > chemteam > mdanalysis_distance

annotate distance.xml @ 9:fd987ff06ceb draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
author chemteam
date Fri, 13 Nov 2020 19:42:40 +0000
parents ffd6f8d159e1
children
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ffd6f8d159e1 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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1 <tool id="mdanalysis_distance" name="Distance Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
4
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2 <description>- time series using MDAnalysis</description>
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3 <macros>
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4 <import>macros.xml</import>
7
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
5
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10 #if $inps.inps == 'one':
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11 python '$__tool_directory__/distance_single.py'
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12 --isegid1 '$inps.segid1'
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13 --iresid1 '$inps.resid1'
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14 --iname1 '$inps.name1'
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15 --isegid2 '$inps.segid2'
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16 --iresid2 '$inps.resid2'
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17 --iname2 '$inps.name2'
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18 --odistance_plot '$distance_plot'
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19 2>&1
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20 #elif $inps.inps == 'multiple':
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21 python '$__tool_directory__/distance_multiple.py'
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22 --list1 '$inps.list1'
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23 --list2 '$inps.list2'
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24 #end if
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25 --itraj '$trajin'
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26 --istr '$strin'
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27 --itrajext '$trajin.ext'
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28 --istrext '$strin.ext'
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29 --output '$output'
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30 $header
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31
0
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32 ]]></command>
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33 <inputs>
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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34 <expand macro="analysis_inputs"/>
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35
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36 <conditional name="inps">
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37 <param argument="inps" type="select" label="Number of pairwise distances to calculate?">
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38 <option value="one" selected="true">One</option>
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39 <option value="multiple">Multiple</option>
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40 </param>
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41 <when value="one">
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42 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
d540ea77b909 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 12823af06b7926cc56aaf9b59cfea9f16d342b8c"
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43 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
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44 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
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45 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
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46 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
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47 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
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48 </when>
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49 <when value="multiple">
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50 <param name="list1" type="data" format="text" label="Selection groups (list 1)"/>
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51 <param name="list2" type="data" format="text" label="Selection groups (list 2)"/>
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52 </when>
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53 </conditional>
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54 <param name="header" type="boolean" truevalue="--header" falsevalue="" label="Include header in output file"/>
0
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55 </inputs>
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56 <outputs>
5
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57 <data format="tabular" name="output" label="Distance Analysis raw data"/>
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58 <data format="png" name="distance_plot" label="Distance Analysis Plot">
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59 <filter>inps == 'one'</filter>
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60 </data>
0
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61 </outputs>
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62 <tests>
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63 <test>
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64 <expand macro="tests_inputs"/>
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65 <param name="segid1" value="PRO"/>
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66 <param name="resid1" value="212"/>
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67 <param name="name1" value="OE2"/>
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68 <param name="segid2" value="HET"/>
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69 <param name="resid2" value="3"/>
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70 <param name="name2" value="C1"/>
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71 <param name="header" value="false"/>
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72 <output name="output" file="Distance_Analysis_raw_data.tabular" />
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73 </test>
4
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74 <test>
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75 <expand macro="tests_inputs_gmx"/>
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76 <param name="segid1" value="SYSTEM"/>
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77 <param name="resid1" value="212"/>
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78 <param name="name1" value="OE2"/>
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79 <param name="segid2" value="SYSTEM"/>
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80 <param name="resid2" value="3"/>
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81 <param name="name2" value="C1"/>
5
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82 <param name="header" value="false"/>
4
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83 <output name="output">
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84 <assert_contents>
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85 <has_n_columns n="2" />
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86 <has_line_matching expression="0\s+3.893.*" />
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87 <has_line_matching expression="14\s+3.262.*" />
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88 </assert_contents>
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89 </output>
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90 </test>
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91 <test>
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92 <expand macro="tests_inputs_gmx"/>
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93 <param name="inps" value="multiple"/>
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94 <param name="list1" value="list1.txt"/>
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95 <param name="list2" value="list2.txt"/>
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96 <param name="header" value="true"/>
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97 <output name="output">
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98 <assert_contents>
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99 <has_n_columns n="2" />
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100 <has_line_matching expression="Frame\s+resid_212_and_name_OE2-resid_3_and_name_C1" />
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101 <has_line_matching expression="0\s+3.893.*" />
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102 <has_line_matching expression="14\s+3.262.*" />
4
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103 </assert_contents>
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104 </output>
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105 </test>
0
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106 </tests>
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107 <help><![CDATA[
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108 .. class:: infomark
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109
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110 **What it does**
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111
5
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112 This tool calculates and plots the distance between pairs of atoms. Two modes are
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113 available: single pair mode, where distances are calculated between two specified
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114 atoms, and multiple pair mode, where two lists of atoms need to be provided.
0
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115
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116 _____
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117
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118
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119 .. class:: infomark
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120
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121 **Input**
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122
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123 - Trajectory file (DCD).
c33b972fe040 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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124 - PDB file.
5
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125
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126 In single pair mode, segment IDs, residue IDs and names of two atoms are selected.
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127 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one
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128 protein or all the solvent molecules or simply the whole system.
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129
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130 In multiple pair mode, two files need to be uploaded, each with one or more atom
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131 groups defined using the MDAnalysis atom selection, each on a new line. For example:
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132
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133 ::
4
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134
5
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135 resid 163
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136 resid 56
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137 resid 12 and type N
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138
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139 All possible distances between the two sets of atom groups will be calculated. For
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140 example, if List 1 contains 5 atoms and List 2 contains 8 atoms, the output file will
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141 contain 40 columns, each with the distance between one group in List 1 and one group
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142 in List 2.
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143
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144 Note that in multiple pair mode, if the group has multiple atoms, the center of mass
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145 will be used for the calculation.
4
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146
0
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147 _____
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148
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149
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150 .. class:: infomark
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151
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152 **Output**
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153
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154 - Tab-separated file of raw data of distance between two atoms calculated for each frame.
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155 - Image (as png) of the time series graph.
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156
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157
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158 ]]></help>
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159 <expand macro="citations" />
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160 </tool>