Mercurial > repos > marpiech > norwich_tools_dock

annotate acpc.xml @ 3:8c2e85bb2ce9 draft

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planemo upload commit 489ad526806f22eefcb73e8d8efe44d648e8185e-dirty
author marpiech
date Tue, 20 Sep 2016 09:57:24 -0400
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3
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1 <tool id="acpc" name="ACPC" version="1.0">
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2 <description>Chemoinformatics tool for ligand-based virtual screening</description>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command>
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7 <![CDATA[
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8 #if $program_chose.program=="acpc" #
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9 if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then
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10 cat $program_chose.q > query.mol2;
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11 cat $program_chose.db > database.mol2 ;
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12 else
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13 if cat $program_chose.q | grep "BEGIN" > /dev/null; then
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14 cat $program_chose.q > query.pl;
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15 cat $program_chose.db > database.pl ;
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16 else
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17 cat $program_chose.q > query.pqr;
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18 cat $program_chose.db > database.pqr ;
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19 fi;
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20 fi;
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21 acpc
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22 -q query.*
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23 -db database.*
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24 #if $program_chose.top_mol.top_scoring_mol=="true"
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25 -top $program_chose.top_mol.top
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26 -o mol_output
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27 #end if
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28 #if $program_chose.a
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29 -a $program_chose.a
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30 #end if
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31 #if $program_chose.nopp=="true"
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32 -nopp
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33 #end if
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34 #if $program_chose.er
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35 -er $program_chose.er
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36 #end if
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37 #if $program_chose.scan=="true"
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38 -scan scan_out
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39 #end if
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40 -v
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41 ;
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42 cat *.scores > $score_output_acpc;
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43 #if $program_chose.top_mol.top_scoring_mol=="true" #
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44 cat mol_output > $mol_output_acpc;
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45 #end if #
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46 #if $program_chose.scan=="true" #
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47 cat scan_out > $scan_output_acpc;
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48 cat query.mol2.bld > $bld_output_acpc;
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49 #end if #
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50 #end if #
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51 #if $program_chose.program=="acpc_mol2tool" #
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52 cat $program_chose.i > query.mol2;
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53 acpc_mol2tool -i query.mol2;
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54 mkdir results;
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55 mv query_*/* results/. ;
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56 #end if #
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57 #if $program_chose.program=="acpc_par" #
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58 if cat $program_chose.q | grep "@<TRIPOS>" > /dev/null; then
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59 cat $program_chose.q > query.mol2;
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60 cat $program_chose.db > database.mol2 ;
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61 else
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62 if cat $program_chose.q | grep "BEGIN" > /dev/null; then
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63 cat $program_chose.q > query.pl;
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64 cat $program_chose.db > database.pl ;
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65 else
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66 cat $program_chose.q > query.pqr;
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67 cat $program_chose.db > database.pqr ;
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68 fi;
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69 fi;
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70 acpc_par
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71 -q query.*
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72 -db database.*
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73 -o score
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74 #if $program_chose.a
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75 -a $a
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76 #end if
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77 #if $program_chose.np
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78 -np $np
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79 #end if
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80 ;
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81 cat score > $output_acpc_par;
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82 #end if #
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83 #if $program_chose.program=="acpc_pqrtool" #
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84 cat $program_chose.pqrfile > pqrfile.pqr;
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85 acpc_pqrtool pqrfile.pqr > $output_acpc_pqrtool;
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86 #end if #
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87 #if $program_chose.program=="acpc_mol2reader" #
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88 cat $program_chose.mol2file > mol2file.mol2;
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89 acpc_mol2reader mol2file.mol2 > $output_acpc_mol2reader;
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90 #end if #
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91 #if $program_chose.program=="acpc_auctool" #
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92 cat $program_chose.i > score.scores;
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93 acpc_auctool -i score.scores -p $program_chose.p > $output_acpc_auctool;
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94 #end if #
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95 #if $program_chose.program=="acpc_pltool" #
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96 cat $program_chose.plfile > plfile.pl;
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97 acpc_pltool plfile.pl > $output_acpc_pltool;
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98 #end if #
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99
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100 ]]>
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101 </command>
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102 <inputs>
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103 <conditional name="program_chose">
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104 <param name="program" type="select" label="Chose a program ">
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105 <option value="acpc" selected="true">acpc </option>
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106 <!-- <option value="acpc_consrank">acpc_consrank </option> -->
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107 <option value="acpc_mol2tool">acpc_mol2tool </option>
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108 <option value="acpc_pqrtool">acpc_pqrtool </option>
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109 <option value="acpc_auctool">acpc_auctool </option>
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110 <!-- <option value="acpc_ertool">acpc_ertool </option> -->
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111 <option value="acpc_par">acpc_par </option>
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112 <!-- <option value="acpc_scorer">acpc_scorer </option> -->
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113 <!-- <option value="acpc_codec">acpc_codec </option> -->
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114 <option value="acpc_mol2reader">acpc_mol2reader </option>
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115 <option value="acpc_pltool">acpc_pltool </option>
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116 </param>
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117 <when value="acpc">
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118 <param name="q" type="data" format="mol2,pqr,pl" label="Query" help="acpc (-q)" />
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119 <param name="db" type="data" format="mol2,pqr,pl" label="Database" help="acpc (-db)" />
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120 <param name="a" type="float" label="Kernel parameter (default depends on considered feature space and was optimized on DUD-E)" help="acpc (-a)" optional="true" />
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121 <param name="er" type="float" label="Enrichment rate parameter; e.g. 0.01 --> ER_1%" help="acpc (-er)" optional="true">
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122 <validator type="in_range" min="0" max="1" />
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123 </param>
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124 <param name="nopp" type="select" label="Don't rm duplicate molecules (based on names)" help="acpc (-nopp)">
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125 <option value="false" selected="true">Don't use this option</option>
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126 <option value="true">Use this option</option>
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127 </param>
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128 <param name="scan" type="select" label="Scan delta AUC per atom in the query and create a new query molecule" help="acpc (-scan)">
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129 <option value="false" selected="true">Don't use this option</option>
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130 <option value="true">Use this option</option>
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131 </param>
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132 <conditional name="top_mol" >
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133 <param name="top_scoring_mol" type="select" label="Return file with top scoring molecules (only works for MOL2 files)" >
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134 <option value="false" selected="true">Don't use this option</option>
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135 <option value="true">Use this option</option>
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136 </param>
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137 <when value="false" >
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138 </when>
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139 <when value="true" >
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140 <param name="top" type="integer" value="1" label="Number of top scoring molecules to output" help="acpc (-top)" />
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141 </when>
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142 </conditional>
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143 </when>
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144 <!-- <when value="acpc_consrank"> -->
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145 <!-- </when> -->
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146 <when value="acpc_mol2tool">
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147 <param name="i" type="data" format="mol2" label="Input mol2 file" help="acpc_mol2tool (-i)" />
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148 </when>
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149 <when value="acpc_pqrtool">
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150 <param name="pqrfile" type="data" format="pqr" label="Input pqr file" />
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151 </when>
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152 <when value="acpc_auctool">
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153 <param name="i" type="data" format="data" label="Input score file" />
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154 <param name="p" type="text" value="0.05" label="A float such that x in (0.0; 1.0] " />
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155 </when>
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156 <!-- <when value="acpc_ertool"> -->
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157 <!-- </when> -->
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158 <when value="acpc_par">
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159 <param name="q" type="data" format="mol2" label="Query" help="acpc_par (-q)" />
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160 <param name="db" type="data" format="mol2" label="Database" help="acpc_par (-db)" />
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161 <param name="a" type="float" label="Kernel parameter (default depends on considered feature space and was optimized on DUD-E)" help="acpc_par (-a)" optional="true" />
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162 <param name="np" type="integer" label="Max number of cores to use" help="acpc_par (-np)" optional="true" />
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163 </when>
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164 <!-- <when value="acpc_scorer"> -->
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165 <!-- </when> -->
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166 <!-- <when value="acpc_codec"> -->
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167 <!-- </when> -->
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168 <when value="acpc_mol2reader">
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169 <param name="mol2file" type="data" format="mol2" label="Input mol2 file" />
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170 </when>
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171 <when value="acpc_pltool">
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172 <param name="plfile" type="data" format="pl" label="Input pl file" />
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173 </when>
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174 </conditional>
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175 </inputs>
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176 <outputs>
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177 <data name="mol_output_acpc" format="txt" label="ACPC: output molecules" >
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178 <filter>program_chose["program"]=="acpc" and program_chose["top_mol"]["top_scoring_mol"]=="true"</filter>
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179 </data>
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180 <data name="score_output_acpc" format="txt" label="ACPC: score" >
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181 <filter>program_chose["program"]=="acpc"</filter>
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182 </data>
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183 <data name="scan_output_acpc" format="txt" label="ACPC: scan file">
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184 <filter>program_chose["program"]=="acpc" and program_chose["scan"]=="true"</filter>
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185 </data>
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186 <data name="bld_output_acpc" format="txt" label="ACPC: mol2.bld file">
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187 <filter>program_chose["program"]=="acpc"</filter>
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188 <filter>program_chose["scan"]=="true"</filter>
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189 </data>
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190 <data format="txt" name="report">
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191 <filter>program_chose["program"]=="acpc_mol2tool"</filter>
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192 <discover_datasets pattern="([0123456789]*)\.mol2" directory="results" visible="true" />
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193 </data>
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194 <data name="output_acpc_par" format="txt" label="ACPC: score file">
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195 <filter>program_chose["program"]=="acpc_par" </filter>
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196 </data>
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197 <data name="output_acpc_mol2reader" format="txt" label="ACPC mol2reader output">
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198 <filter>program_chose["program"]=="acpc_mol2reader" </filter>
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199 </data>
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200 <data name="output_acpc_pltool" format="txt" label="ACPC pltool output">
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201 <filter>program_chose["program"]=="acpc_pltool" </filter>
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202 </data>
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203 <data name="output_acpc_auctool" format="txt" label="ACPC auctool output">
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204 <filter>program_chose["program"]=="acpc_auctool" </filter>
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205 </data>
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206 <data name="output_acpc_pqrtool" format="txt" label="ACPC pqrtool output">
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207 <filter>program_chose["program"]=="acpc_pqrtool" </filter>
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208 </data>
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209 </outputs>
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210 <tests>
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211 <test>
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212 <param name="program" value="acpc" />
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213 <param name="top_scoring_mol" value="true" />
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214 <param name="q" value="acpc/query.mol2" />
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215 <param name="db" value="acpc/database.mol2" />
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216 <output name="mol_output_acpc" file="acpc/output"/>
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217 </test>
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218 <test>
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219 <param name="program" value="acpc_mol2reader" />
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220 <param name="mol2file" value="acpc/query.mol2" />
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221 <output name="output_acpc_mol2reader" file="acpc/output_mol2reader"/>
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222 </test>
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223 </tests>
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224 <help>
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225 <![CDATA[
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226 ************
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227 Description
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228 ************
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229 ACPC is a ligand-based virtual screening tool using AutoCorrelation of Partial Charges.
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230
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231 *******
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232 Help
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233 *******
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234
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235 acpc
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236
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237 --a float kernel parameter (default depends on considered feature space and was optimized on DUD-E)
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238 --db db database in .mol2, .pl or .pqr format
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239 --er x enrichment rate parameter; e.g. 0.01 --> ER_1%
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240 --nopp don't rm duplicate molecules (based on names)
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241 --q query query in .mol2, .pl or .pqr format
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242 --scan out_file scan delta AUC per atom in the query and create a new query molecule
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243 --top int number of top scoring molecules to output (only works for MOL2 files)
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244
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245
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246 acpc_mol2tool
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247
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248 --i in input mol2 file
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249
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250 acpc_auctool
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251
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252 -i in input scores file
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253 -p x a float such that 0.0 < x <= 1.0
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254
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255
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256
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257 acpc_par
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258
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259 --a float kernel parameter (default was optimized on DUD-E and depends on considered feature space)
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260 --db db molecules database in .mol2, .pl or .pqr format
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261 --q query molecule in .mol2, .pl or .pqr format
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262 --np int max number of cores to use
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263
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264 ]]>
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265 </help>
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266 <citations>
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267 <citation type="bibtex">
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268 @article{Berenger2014,
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269 doi = {10.1186/1758-2946-6-23},
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270 url = {http://dx.doi.org/10.1186/1758-2946-6-23},
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271 year = {2014},
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272 publisher = {Springer Nature},
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273 volume = {6},
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274 number = {1},
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275 pages = {23},
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276 author = {Francois Berenger and Arnout Voet and Xiao Lee and Kam YJ Zhang},
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277 title = {A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening},
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278 journal = {Journal of Cheminformatics}
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279 }
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280 </citation>
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281 </citations>
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282 </tool>