Mercurial > repos > metexplore > met4j

annotate build/tools/SetNames/SetNames.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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children 6a112eaf8f38
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9
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_SetNames" name="SetNames" version="develop">
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3 <description>Set names to network objects in a SBML file from a tabulated file containing the object ids and the names</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.SetNames#if str($colname) != 'nan':
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11 -cname "$colname"
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12 #end if
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13 #if str($colid):
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14 -ci "$colid"
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15 #end if
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16 $p
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17 $s
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18 #if str($o):
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19 -t "$o"
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20 #end if
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21 #if str($nSkip):
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22 -n "$nSkip"
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23 #end if
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24 -i "$sbml"
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25 #if str($tab) != 'None':
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26 -tab "$tab"
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27 #end if
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28 #if str($c):
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29 -c "$c"
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30 #end if
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31 -o "$out"
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32 ]]></command>
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33 <inputs>
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34 <param argument="-cname" label="[2] number of the column where are the names" name="colname" optional="true" type="integer" value="2"/>
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35 <param argument="-ci" label="[1] number of the column where are the object ids" name="colid" optional="true" type="text" value="1">
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36 <sanitizer invalid_char="_">
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37 <valid initial="string.printable"/>
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38 </sanitizer>
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39 </param>
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40 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix R_ to reactions and M_ to metabolites" name="p" truevalue="-p" type="boolean" value="false"/>
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41 <param argument="-s" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the suffix _comparmentID to metabolites" name="s" truevalue="-s" type="boolean" value="false"/>
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42 <param argument="-t" label="[REACTION] Object type in the column id : REACTION;METABOLITE;GENE;PATHWAY" name="o" optional="true" type="text" value="REACTION">
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43 <sanitizer invalid_char="_">
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44 <valid initial="string.printable"/>
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45 </sanitizer>
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46 </param>
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47 <param argument="-n" label="[0] Number of lines to skip at the beginning of the tabulated file" name="nSkip" optional="true" type="text" value="0">
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48 <sanitizer invalid_char="_">
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49 <valid initial="string.printable"/>
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50 </sanitizer>
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51 </param>
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52 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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53 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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54 <param argument="-c" label="[#] Comment String in the tabulated file. The lines beginning by this string won't be read" name="c" optional="true" type="text" value="#">
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55 <sanitizer invalid_char="_">
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56 <valid initial="string.printable"/>
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57 </sanitizer>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data format="sbml" name="out"/>
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62 </outputs>
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63 <tests>
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64 <test>
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71 <param name="sbml" value="toy_model.xml"/>
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78 <param name="tab" value="namesMetabolites.tsv"/>
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85 <param name="o" value="METABOLITE"/>
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92 <output ftype="sbml" name="out">
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98
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metexplore
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99 <assert_contents>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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100
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101
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102
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103
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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104
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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105
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
parents:
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106 <is_valid_xml/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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107
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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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metexplore
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113 <has_line_matching expression=".*metaboliteA.*" n="1"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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114
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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
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metexplore
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120 <has_line_matching expression=".*metaboliteB.*" n="1"/>
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121
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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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metexplore
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127 </assert_contents>
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128
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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 </output>
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135
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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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metexplore
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141 </test>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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142 <test>
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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 <param name="sbml" value="toy_model.xml"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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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 <param name="tab" value="namesReactions.tsv"/>
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 <output ftype="sbml" name="out">
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
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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169
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170 <assert_contents>
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171
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172
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174
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175
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176
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177 <is_valid_xml/>
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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
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metexplore
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184 <has_line_matching expression=".*reaction1.*" n="1"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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185
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186
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188
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189
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190
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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191 <has_line_matching expression=".*reaction2.*" n="1"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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192
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
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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197
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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198 </assert_contents>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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199
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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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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204
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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205 </output>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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211
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metexplore
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212 </test>
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metexplore
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213 <test>
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214
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216
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metexplore
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220 <param name="sbml" value="XF_network.sbml"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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221
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223
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224
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225
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226
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metexplore
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227 <param name="tab" value="namesPathways.tsv"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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228
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229
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230
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231
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232
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233
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metexplore
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234 <param name="o" value="PATHWAY"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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235
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236
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238
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239
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240
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metexplore
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241 <output ftype="sbml" name="out">
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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242
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243
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246
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247
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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248 <assert_contents>
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249
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250
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251
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252
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253
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254
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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255 <is_valid_xml/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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256
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257
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258
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260
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261
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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262 <has_line_matching expression=".*groups:name=.CEB.*" n="1"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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263
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264
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265
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267
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268
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metexplore
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269 <has_line_matching expression=".*groups:name=.NSP.*" n="1"/>
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270
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271
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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272
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273
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274
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275
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metexplore
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276 </assert_contents>
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277
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278
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279
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282
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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diff changeset
283 </output>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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285
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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286
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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288
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289
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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diff changeset
290 </test>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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291 <test>
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292
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294
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295
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296
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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297
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
parents:
diff changeset
298 <param name="sbml" value="XF_network.sbml"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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299
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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301
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302
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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303
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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304
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
parents:
diff changeset
305 <param name="tab" value="namesGenes.tsv"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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306
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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307
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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308
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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309
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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310
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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311
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
parents:
diff changeset
312 <param name="o" value="GENE"/>
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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313
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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314
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
metexplore
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315
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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316
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319 <output ftype="sbml" name="out">
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320
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326 <assert_contents>
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333 <is_valid_xml/>
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335
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337
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340 <has_line_matching expression=".*fbc:name=.G1.*" n="1"/>
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347 <has_line_matching expression=".*fbc:name=.G2.*" n="1"/>
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354 </assert_contents>
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361 </output>
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368 </test>
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369 </tests>
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370 <help><![CDATA[Set names to network objects in a SBML file from a tabulated file containing the object ids and the names
0976a6257300 planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 05db35f63cadb9d56dafff594a3507c59cd85273
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371 The ids must correspond between the tabulated file and the SBML file.
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372 If prefix or suffix is different in the SBML file, use the -p or the -s options.
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373 ]]></help>
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374 <citations/>
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375 </tool>