Mercurial > repos > metexplore > met4j

annotate build/tools/ExtractAnnotations/ExtractAnnotations.xml @ 9:0976a6257300 draft

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
author metexplore
date Fri, 31 Jan 2025 18:28:53 +0000
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_ExtractAnnotations" name="ExtractAnnotations" version="develop">
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3 <description>Extract databases' references from SBML annotations or notes.</description>
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4 <xrefs>
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5 <xref type="bio.tools">met4j</xref>
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6 </xrefs>
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7 <requirements>
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8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:develop</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.ExtractAnnotations -i "$inputPath"
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11 -export "$export"
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12 -db "$db"
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13 $uniq
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14 $skip
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15 -o "$outputPath"
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16 ]]></command>
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17 <inputs>
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18 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/>
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19 <param argument="-export" label="the type of entity to extract annotation, either metabolite, reaction, or gene" name="export" optional="false" type="select" value="METABOLITE">
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20 <option selected="true" value="METABOLITE">METABOLITE</option>
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21 <option value="REACTION">REACTION</option>
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22 <option value="GENE">GENE</option>
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23 </param>
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24 <param argument="-db" label="name of the referenced database to export annotations from, as listed in notes or identifiers.org base uri" name="db" optional="false" type="text" value="">
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25 <sanitizer invalid_char="_">
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26 <valid initial="string.printable"/>
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27 </sanitizer>
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28 </param>
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29 <param argument="-uniq" checked="false" falsevalue="" label="keep only one identifier if multiple are referenced for the same entity" name="uniq" truevalue="-uniq" type="boolean" value="false"/>
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30 <param argument="-skip" checked="false" falsevalue="" label="Skip entities without the selected annotations, by default output them with NA value" name="skip" truevalue="-skip" type="boolean" value="false"/>
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31 </inputs>
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32 <outputs>
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33 <data format="tsv" name="outputPath"/>
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34 </outputs>
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35 <tests>
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36 <test>
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43 <param name="inputPath" value="Human-GEM_pathways.xml"/>
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50 <param name="export" value="METABOLITE"/>
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57 <param name="db" value="metanetx.chemical"/>
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64 <output ftype="tsv" name="outputPath">
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71 <assert_contents>
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78 <has_n_lines n="146"/>
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85 <has_n_columns n="2"/>
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92 </assert_contents>
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99 </output>
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102
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103
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104
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105
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metexplore
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106 </test>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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107 <test>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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108
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109
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110
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111
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112
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113
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metexplore
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114 <param name="inputPath" value="Human-GEM_pathways.xml"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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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
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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120
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metexplore
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121 <param name="export" value="METABOLITE"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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122
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123
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124
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125
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126
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127
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metexplore
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128 <param name="db" value="metanetx.chemical"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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129
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130
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131
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132
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133
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134
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135 <param name="skip" value="true"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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136
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137
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138
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139
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140
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141
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metexplore
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142 <output ftype="tsv" name="outputPath">
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143
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144
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145
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146
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147
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148
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metexplore
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149 <assert_contents>
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150
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151
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152
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153
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154
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155
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metexplore
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156 <has_n_lines n="145"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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157
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158
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159
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160
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161
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162
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metexplore
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163 <has_n_columns n="2"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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164
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165
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166
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167
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168
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169
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metexplore
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170 </assert_contents>
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171
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172
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173
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174
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175
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176
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metexplore
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177 </output>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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178
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179
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181
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182
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183
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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184 </test>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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185 <test>
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186
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187
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188
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190
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191
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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192 <param name="inputPath" value="Human-GEM_pathways.xml"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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193
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194
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195
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196
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197
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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198
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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199 <param name="export" value="METABOLITE"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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200
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201
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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202
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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203
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204
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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205
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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206 <param name="db" value="metanetx.chemical"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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207
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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208
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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213 <param name="skip" value="true"/>
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220 <param name="uniq" value="true"/>
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227 <output ftype="tsv" name="outputPath">
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234 <assert_contents>
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241 <has_n_lines n="111"/>
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248 <has_n_columns n="2"/>
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255 </assert_contents>
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262 </output>
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269 </test>
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270 </tests>
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271 <help><![CDATA[Extract databases' references from SBML annotations or notes. The references are exported as a tabulated file with one column with the SBML compound, reaction or gene identifiers, and one column with the corresponding database identifier.The name of the targeted database need to be provided under the same form than the one used in the notes field or the identifiers.org uri.]]></help>
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272 <citations/>
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273 </tool>