Mercurial > repos > chemteam > mdanalysis_ramachandran_plot

annotate ramachandran_plots.xml @ 0:d710c7f00ae6 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
author chemteam
date Wed, 03 Apr 2019 15:46:32 -0400
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children ce0728b92289
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0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="0.1.3">
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2 <description>Calculate and plot the distribution of two diheadrals in a trajectory</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.2.1">scipy</requirement>
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8 <requirement type="package" version="0.9.0">seaborn</requirement>
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9 <requirement type="package" version="1.0.5">nbdime</requirement>
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10 </expand>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 python '$__tool_directory__/ramachandran_plots.py'
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14 --idcd '$dcdin'
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15 --ipdb '$pdbin'
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16 --isegid1 '$phi.segid1'
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17 --iresid1 '$phi.resid1'
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18 --iname1 '$phi.name1'
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19 --isegid2 '$phi.segid2'
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20 --iresid2 '$phi.resid2'
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21 --iname2 '$phi.name2'
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22 --isegid3 '$phi.segid3'
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23 --iresid3 '$phi.resid3'
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24 --iname3 '$phi.name3'
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25 --isegid4 '$phi.segid4'
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26 --iresid4 '$phi.resid4'
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27 --iname4 '$phi.name4'
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28 --isegid5 '$psi.segid1'
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29 --iresid5 '$psi.resid1'
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30 --iname5 '$psi.name1'
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31 --isegid6 '$psi.segid2'
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32 --iresid6 '$psi.resid2'
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33 --iname6 '$psi.name2'
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34 --isegid7 '$psi.segid3'
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35 --iresid7 '$psi.resid3'
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36 --iname7 '$psi.name3'
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37 --isegid8 '$psi.segid4'
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38 --iresid8 '$psi.resid4'
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39 --iname8 '$psi.name4'
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40 --output '$output'
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41 --oramachandran_plot '$ramachandran_plot'
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42 2>&1
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43 ]]></command>
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44 <inputs>
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45 <expand macro="analysis_inputs"/>
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46 <section name="phi" title="Phi" expanded="False">
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47 <param name="segid1" type="text" value="HET" label="Segid of atom 1">
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48 <expand macro="sanitizer"/>
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49 </param>
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50 <param name="resid1" type="text" value="3" label="Resid of atom 1">
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51 <expand macro="sanitizer_resids"/>
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52 </param>
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53 <param name="name1" type="text" value="O5" label="Atom name of atom 1">
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54 <expand macro="sanitizer"/>
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55 </param>
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56 <param name="segid2" type="text" value="HET" label="Segid of atom 2">
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57 <expand macro="sanitizer"/>
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58 </param>
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59 <param name="resid2" type="text" value="3" label="Resid of atom 2">
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60 <expand macro="sanitizer_resids"/>
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61 </param>
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62 <param name="name2" type="text" value="C1" label="Atom name of atom 2">
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63 <expand macro="sanitizer"/>
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64 </param>
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65 <param name="segid3" type="text" value="HET" label="Segid of atom 3">
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66 <expand macro="sanitizer"/>
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67 </param>
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68 <param name="resid3" type="text" value="2" label="Resid of atom 3">
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69 <expand macro="sanitizer_resids"/>
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70 </param>
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71 <param name="name3" type="text" value="O4" label="Atom name of atom 3">
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72 <expand macro="sanitizer"/>
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73 </param>
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74 <param name="segid4" type="text" value="HET" label="Segid of atom 4">
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75 <expand macro="sanitizer"/>
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76 </param>
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77 <param name="resid4" type="text" value="2" label="Resid of atom 4">
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78 <expand macro="sanitizer_resids"/>
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79 </param>
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80 <param name="name4" type="text" value="C4" label="Atom name of atom 4">
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81 <expand macro="sanitizer"/>
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82 </param>
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83 </section>
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84 <section name="psi" title="Psi" expanded="False">
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85 <param name="segid1" type="text" value="HET" label="Segid of atom 1">
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86 <expand macro="sanitizer"/>
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87 </param>
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88 <param name="resid1" type="text" value="3" label="Resid of atom 1">
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89 <expand macro="sanitizer_resids"/>
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90 </param>
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91 <param name="name1" type="text" value="C1" label="Atom name of atom 1">
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92 <expand macro="sanitizer"/>
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93 </param>
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94 <param name="segid2" type="text" value="HET" label="Segid of atom 2">
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95 <expand macro="sanitizer"/>
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96 </param>
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97 <param name="resid2" type="text" value="2" label="Resid of atom 2">
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98 <expand macro="sanitizer_resids"/>
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99 </param>
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100 <param name="name2" type="text" value="O4" label="Atom name of atom 2">
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101 <expand macro="sanitizer"/>
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102 </param>
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103 <param name="segid3" type="text" value="HET" label="Segid of atom 3">
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104 <expand macro="sanitizer"/>
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105 </param>
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106 <param name="resid3" type="text" value="2" label="Resid of atom 3">
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107 <expand macro="sanitizer_resids"/>
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108 </param>
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109 <param name="name3" type="text" value="C4" label="Atom name of atom 3">
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110 <expand macro="sanitizer"/>
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111 </param>
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112 <param name="segid4" type="text" value="HET" label="Segid of atom 4">
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113 <expand macro="sanitizer"/>
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114 </param>
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115 <param name="resid4" type="text" value="2" label="Resid of atom 4">
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116 <expand macro="sanitizer_resids"/>
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117 </param>
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118 <param name="name4" type="text" value="C3" label="Atom name of atom 4">
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119 <expand macro="sanitizer"/>
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120 </param>
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121 </section>
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122 </inputs>
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123 <outputs>
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124 <data format="tabular" name="output" label="Ramachandran Plot raw data"/>
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125 <data format="png" name="ramachandran_plot" label="Ramachandran Plot"/>
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126 </outputs>
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127 <tests>
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128 <test>
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129 <expand macro="tests_inputs"/>
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130 <param name="phi.segid1" value="HET"/>
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131 <param name="phi.resid1" value="3"/>
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132 <param name="phi.name1" value="O5"/>
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133 <param name="phi.segid2" value="HET"/>
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134 <param name="phi.resid2" value="3"/>
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135 <param name="phi.name2" value="C1"/>
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136 <param name="phi.segid3" value="HET"/>
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137 <param name="phi.resid3" value="2"/>
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138 <param name="phi.name3" value="O4"/>
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139 <param name="phi.segid4" value="HET"/>
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140 <param name="phi.resid4" value="2"/>
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141 <param name="phi.name4" value="C4"/>
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142 <param name="psi.segid1" value="HET"/>
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143 <param name="psi.resid1" value="3"/>
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144 <param name="psi.name1" value="C1"/>
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145 <param name="psi.segid2" value="HET"/>
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146 <param name="psi.resid2" value="2"/>
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147 <param name="psi.name2" value="O4"/>
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148 <param name="psi.segid3" value="HET"/>
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149 <param name="psi.resid3" value="2"/>
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150 <param name="psi.name3" value="C4"/>
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151 <param name="psi.segid4" value="HET"/>
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152 <param name="psi.resid4" value="2"/>
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153 <param name="psi.name4" value="C3"/>
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154 <output name="output" file="Ramachandran_Plot_raw_data.tabular" />
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155 </test>
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156 </tests>
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157 <help><![CDATA[
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158 .. class:: infomark
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159
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160 **What it does**
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161
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162 A Ramachandran plot ([φ,ψ] plot), originally developed as a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid.
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163 This can be also used to calculate glycosidic φ and ψ angles formed between carbohydrates. This tool can calculate and plot the histogram (ramachandran plot) of user define φ and ψ angles of a trajectory.
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164
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165 - For protien φ and ψ diheadral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html.
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166
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167 - For glycan φ and ψ diheadral definitions see http://www.glycanstructure.org/
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168
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169 _____
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170
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171
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172 .. class:: infomark
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173
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174 **Input**
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175
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176 - Trajectory file (DCD).
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177 - PDB file.
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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178 - Segids, resids and names of the four atoms to calculate diheadrals.
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179
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180 _____
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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181
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182
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183 .. class:: infomark
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184
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185 **Output**
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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186
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187 - Tab-separated file of raw data of the φ,ψ angles time series.
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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188 - Image (as png) of the Ramachandran Plot.
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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189
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190
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191 ]]></help>
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192 <expand macro="citations" />
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193 </tool>