Mercurial > repos > metexplore > met4j

annotate tools/attributes/SetCharges/SetCharges.xml @ 11:40c15b7467f1 draft default tip

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planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy commit 61dbdbae896d18b519a470e056cb8b4f98394518
author metexplore
date Thu, 13 Feb 2025 15:08:22 +0000
parents 6a112eaf8f38
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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2 <tool id="met4j_SetCharges" name="SetCharges" version="2.0.1">
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3 <description>Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges</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:2.0.1</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh attributes.SetCharges#if str($colcharge) != 'nan':
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11 -cc "$colcharge"
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12 #end if
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13 #if str($colid) != 'nan':
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14 -ci "$colid"
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15 #end if
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16 $p
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17 $s
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18 #if str($nSkip):
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19 -n "$nSkip"
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20 #end if
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21 -i "$sbml"
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22 #if str($tab) != 'None':
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23 -tab "$tab"
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24 #end if
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25 #if str($c):
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26 -c "$c"
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27 #end if
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28 -o "$out"
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29 ]]></command>
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30 <inputs>
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31 <param argument="-cc" label="[2] number of the column where are the charges" name="colcharge" optional="true" type="integer" value="2"/>
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32 <param argument="-ci" label="[1] number of the column where are the metabolite ids" name="colid" optional="true" type="integer" value="1"/>
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33 <param argument="-p" checked="false" falsevalue="" label="[deactivated] To match the objects in the sbml file, adds the prefix M_ to metabolite ids" name="p" truevalue="-p" type="boolean" value="false"/>
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34 <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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35 <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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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="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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41 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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42 <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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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 </inputs>
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48 <outputs>
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49 <data format="sbml" name="out"/>
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50 </outputs>
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51 <tests>
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52 <test>
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53
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54 <param name="sbml" value="toy_model.xml"/>
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56 <param name="tab" value="charges.tsv"/>
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58 <output ftype="sbml" name="out">
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60 <assert_contents>
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62 <is_valid_xml/>
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64 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
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66 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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68 </assert_contents>
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70 </output>
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72 </test>
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73 <test>
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75 <param name="sbml" value="toy_model.xml"/>
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77 <param name="tab" value="chargesWithComment.tsv"/>
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79 <output ftype="sbml" name="out">
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81 <assert_contents>
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83 <is_valid_xml/>
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85 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
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87 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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89 </assert_contents>
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91 </output>
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93 </test>
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94 <test>
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95
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96 <param name="sbml" value="toy_model.xml"/>
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97
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98 <param name="tab" value="charges.tsv"/>
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99
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100 <param name="nSkip" value="1"/>
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101
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102 <output ftype="sbml" name="out">
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103
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104 <assert_contents>
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105
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106 <is_valid_xml/>
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107
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108 <has_line_matching expression=".*fbc:charge=.2.*" n="1" negate="true"/>
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109
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110 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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111
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112 </assert_contents>
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113
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114 </output>
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115
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116 </test>
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117 <test>
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118
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119 <param name="sbml" value="toy_model.xml"/>
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120
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121 <param name="tab" value="charges.tsv"/>
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122
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123 <param name="ci" value="2"/>
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124
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125 <param name="cc" value="3"/>
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126
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127 <output ftype="sbml" name="out">
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128
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129 <assert_contents>
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130
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131 <is_valid_xml/>
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132
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133 <has_line_matching expression=".*fbc:charge=.2.*" n="1"/>
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134
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135 <has_line_matching expression=".*fbc:charge=.-3.*" n="1"/>
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136
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137 </assert_contents>
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138
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139 </output>
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140
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141 </test>
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142 <test>
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143
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144 <param name="sbml" value="XF_network.sbml"/>
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145
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146 <param name="tab" value="chargesXF.tsv"/>
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147
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148 <param name="p" value="true"/>
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149
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150 <param name="s" value="true"/>
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151
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152 <output ftype="sbml" name="out">
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153
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154 <assert_contents>
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155
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156 <is_valid_xml/>
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157
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158 <has_line_matching expression=".*fbc:charge=.-1000.*" n="3"/>
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159
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160 </assert_contents>
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161
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162 </output>
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163
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164 </test>
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165 </tests>
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166 <help><![CDATA[Set charge to metabolites in a SBML file from a tabulated file containing the metabolite ids and the charges
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167 The charge must be a number. The ids must correspond between the tabulated file and the SBML file.
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168 If prefix or suffix is different in the SBML file, use the -p or the -s options.
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169 The charge will be written in the SBML file in two locations:+
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170 - in the reaction notes (e.g. charge: -1)
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171 - as fbc attribute (e.g. fbc:charge="1")]]></help>
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172 <citations>
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173 <citation type="doi">10.1515/jib-2017-0082</citation>
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174 </citations>
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175 </tool>