Mercurial > repos > metexplore > met4j

annotate tools/attributes/SetPathways/SetPathways.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_SetPathways" name="SetPathways" version="2.0.1">
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3 <description>Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways</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.SetPathways#if str($colp) != 'nan':
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11 -cp "$colp"
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12 #end if
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13 #if str($sep):
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14 -sep "$sep"
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15 #end if
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16 #if str($colid) != 'nan':
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17 -ci "$colid"
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18 #end if
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19 $p
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20 #if str($nSkip):
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21 -n "$nSkip"
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22 #end if
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23 -i "$sbml"
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24 #if str($tab) != 'None':
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25 -tab "$tab"
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26 #end if
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27 #if str($c):
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28 -c "$c"
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29 #end if
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30 -o "$out"
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31 ]]></command>
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32 <inputs>
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33 <param argument="-cp" label="[2] number of the column where are the pathways" name="colp" optional="true" type="integer" value="2"/>
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34 <param argument="-sep" label="[|] Separator of pathways in the tabulated file" name="sep" optional="true" type="text" value="|">
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35 <sanitizer invalid_char="_">
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36 <valid initial="string.printable"/>
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37 </sanitizer>
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38 </param>
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39 <param argument="-ci" label="[1] number of the column where are the reaction ids" name="colid" optional="true" type="integer" value="1"/>
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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" name="p" truevalue="-p" type="boolean" value="false"/>
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41 <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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42 <sanitizer invalid_char="_">
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43 <valid initial="string.printable"/>
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44 </sanitizer>
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45 </param>
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46 <param argument="-i" format="sbml" label="Original SBML file" name="sbml" optional="false" type="data" value=""/>
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47 <param argument="-tab" format="tsv" label="Input Tabulated file" name="tab" optional="true" type="data" value=""/>
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48 <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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49 <sanitizer invalid_char="_">
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50 <valid initial="string.printable"/>
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51 </sanitizer>
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52 </param>
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53 </inputs>
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54 <outputs>
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55 <data format="sbml" name="out"/>
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56 </outputs>
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57 <tests>
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58 <test>
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60 <param name="sbml" value="toy_model.xml"/>
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62 <param name="tab" value="pathways.tsv"/>
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64 <output ftype="sbml" name="out">
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66 <assert_contents>
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68 <is_valid_xml/>
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70 <has_line_matching expression=".*groups:id=.*" n="3"/>
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72 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
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74 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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76 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
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78 </assert_contents>
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80 </output>
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82 </test>
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83 <test>
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85 <param name="sbml" value="toy_model.xml"/>
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87 <param name="tab" value="pathwaysOtherSep.tsv"/>
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89 <param name="sep" value=" + "/>
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91 <output ftype="sbml" name="out">
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93 <assert_contents>
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95 <is_valid_xml/>
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96
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97 <has_line_matching expression=".*groups:id=.*" n="3"/>
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98
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99 <has_line_matching expression=".*groups:id=.p1.*" n="1"/>
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100
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101 <has_line_matching expression=".*groups:id=.p2.*" n="1"/>
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102
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103 <has_line_matching expression=".*groups:id=.p3.*" n="1"/>
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104
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105 </assert_contents>
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106
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107 </output>
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108
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109 </test>
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110 </tests>
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111 <help><![CDATA[Set pathway to reactions in a network from a tabulated file containing the reaction ids and the pathways
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112 The ids must correspond between the tabulated file and the SBML file.
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113 If prefix R_ is present in the ids in the SBML file and not in the tabulated file, use the -p option.
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114 Pathways will be written in the SBML file in two ways:- as reaction note (e.g. SUBSYSTEM: purine_biosynthesis)- as SBML group (see Group package specifications: https://pmc.ncbi.nlm.nih.gov/articles/PMC5451322/)]]></help>
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115 <citations>
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116 <citation type="doi">10.1515/jib-2016-290</citation>
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117 </citations>
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118 </tool>