Mercurial > repos > malex > gait_gm
annotate add_kegg_pathway_info.xml @ 2:2c218a253d56 draft default tip
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
| author | malex |
|---|---|
| date | Thu, 29 Jul 2021 20:48:10 +0000 |
| parents | ec9ee8edb84d |
| children |
| rev | line source |
|---|---|
| 1 | 1 <tool id="secimtools_add_kegg_pathway_info" name="Add KEGG Pathway Information" version="@WRAPPER_VERSION@"> |
| 2 <description>using KEGGIDs</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 add_kegg_pathway_info.py | |
| 9 -sp=$species | |
| 10 #if $dataSets.whichDataSet == "geneDataset": | |
| 11 -gka=$dataSets.geneKeggAnnot | |
| 12 -gid=$dataSets.geneUniqId | |
| 13 -gn=$dataSets.geneName | |
| 14 -gkid=$dataSets.geneKeggId | |
| 15 -go=$geneOutput | |
| 16 -kg2p=$gene_keggID2pathID | |
| 17 #end if | |
| 18 #if $dataSets.whichDataSet == "metDataset": | |
| 19 -mka=$dataSets.metKeggAnnot | |
| 20 -mid=$dataSets.metUniqId | |
| 21 -mn=$dataSets.metName | |
| 22 -mkid=$dataSets.metKeggId | |
| 23 -mo=$metOutput | |
| 24 -km2p=$met_keggID2pathID | |
| 25 #end if | |
| 26 #if $dataSets.whichDataSet == "both": | |
| 27 -gka=$dataSets.geneKeggAnnot | |
| 28 -gid=$dataSets.geneUniqId | |
| 29 -gn=$dataSets.geneName | |
| 30 -gkid=$dataSets.geneKeggId | |
| 31 -mka=$dataSets.metKeggAnnot | |
| 32 -mid=$dataSets.metUniqId | |
| 33 -mn=$dataSets.metName | |
| 34 -mkid=$dataSets.metKeggId | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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35 -kg2p=$gene_keggID2pathID |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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36 -km2p=$met_keggID2pathID |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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37 -go=$geneOutput |
| 1 | 38 -mo=$metOutput |
| 39 #end if | |
| 40 -p=$pathways | |
| 41 ]]></command> | |
| 42 <inputs> | |
| 43 <param name="species" type="select" label="Select your Species from the List" > | |
| 44 <option value="hsa">Homo sapiens</option> | |
| 45 <option value="mmu">Mus musculus</option> | |
| 46 <option value="rno">Rattus norvegicus</option> | |
| 47 <option value="dme">Drosophila melanogaster</option> | |
| 48 <option value="ath">Arabidopsis thaliana</option> | |
| 49 <option value="sce">Saccharomyces cerevisiae</option> | |
| 50 <option value="eco">Escherichia coli</option> | |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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51 <option value="cel">Caenorhabditis elegans</option> |
| 1 | 52 </param> |
| 53 <conditional name="dataSets"> | |
| 54 <param name="whichDataSet" type="select" display="radio" label="Select the Datasets you want to add KEGG pathway information to. Note: datasets must contain KEGGIDs."> | |
| 55 <option value="both" selected="true">Gene Expression + Metabolomic Files with KEGGIDs</option> | |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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56 <option value="geneDataset">Gene Expression File with KEGGIDs</option> |
| 1 | 57 <option value="metDataset">Metabolomic File with KEGGIDs</option> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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58 <validator type="no_options" message="You must select at least one option." /> |
| 1 | 59 </param> |
| 60 <when value="both"> | |
| 61 <param name="geneKeggAnnot" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select the Gene to KEGGID Link File that contains KEGG identifiers from your history"/> | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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62 <param name="geneUniqId" type="text" size="30" value="" label="Gene unique FeatureID" help="Name of the column in your Gene to KEGGID Link File that contains unique FeatureIDs."/> |
| 1 | 63 <param name="geneName" type="text" size="30" value="" label="Gene Symbol" help="Name of the column in your Gene to KEGGID Link File that contains Gene Symbols."/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
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64 <param name="geneKeggId" type="text" size="30" value="" label="Gene KEGGID" help="Name of the column in your Gene to KEGGID Link File that contains KEGGIDs."/> |
| 1 | 65 <param name="metKeggAnnot" type="data" format="tabular" label="Metabolite to KEGGID Link File" help="Select the Metabolite to KEGGID Link File that contains KEGG identifiers from your history"/> |
| 66 <param name="metUniqId" type="text" size="30" value="" label="Metabolite unique FeatureID" help="Name of the column in your Metabolite to KEGGID Link File that contains unique FeatureIDs."/> | |
| 67 <param name="metName" type="text" size="30" value="" label="Metabolite Names" help="Name of the column in your Metabolite to KEGGID Link File that contains Metabolite Names."/> | |
| 68 <param name="metKeggId" type="text" size="30" value="" label="Metabolite KEGGID" help="Name of the column in your Metabolite to KEGGID Link File that contains KEGGIDs."/> | |
| 69 </when> | |
| 70 <when value="geneDataset"> | |
| 71 <param name="geneKeggAnnot" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select the Gene to KEGGID Link File that contains KEGG identifiers from your history"/> | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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72 <param name="geneUniqId" type="text" size="30" value="" label="Gene unique FeatureID" help="Name of the column in your Gene to KEGGID Link File that contains unique FeatureIDs."/> |
| 1 | 73 <param name="geneName" type="text" size="30" value="" label="Gene Symbol" help="Name of the column in your Gene to KEGGID Link File that contains Gene Symbols."/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
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74 <param name="geneKeggId" type="text" size="30" value="" label="Gene KEGGID" help="Name of the column in your Gene to KEGGID Link File that contains KEGGIDs."/> |
| 1 | 75 </when> |
| 76 <when value="metDataset"> | |
| 77 <param name="metKeggAnnot" type="data" format="tabular" label="Metabolite to KEGGID Link File" help="Select the Metabolite to KEGGID Link File that contains KEGG identifiers from your history"/> | |
| 78 <param name="metUniqId" type="text" size="30" value="" label="Metabolite unique FeatureID" help="Name of the column in your Metabolite to KEGGID Link File that contains unique FeatureIDs."/> | |
| 79 <param name="metName" type="text" size="30" value="" label="Metabolite Names" help="Name of the column in your Metabolite to KEGGID Link File that contains Metabolite Names."/> | |
| 80 <param name="metKeggId" type="text" size="30" value="" label="Metabolite KEGGID" help="Name of the column in your Metabolite to KEGGID Link File that contains KEGGIDs."/> | |
| 81 </when> | |
| 82 </conditional> | |
| 83 </inputs> | |
| 84 <outputs> | |
| 85 <data format="tabular" name="gene_keggID2pathID" label="${tool.name} on ${on_string}: GeneKeggID2PathwayID"> | |
| 86 <filter>(dataSets['whichDataSet'] == 'geneDataset') or (dataSets['whichDataSet'] == 'both')</filter> | |
| 87 </data> | |
| 88 <data format="tabular" name="met_keggID2pathID" label="${tool.name} on ${on_string}: MetaboliteKeggID2PathwayID"> | |
| 89 <filter>(dataSets['whichDataSet'] == 'metDataset') or (dataSets['whichDataSet'] == 'both')</filter> | |
| 90 </data> | |
| 91 <data format="tabular" name="pathways" label="${tool.name} on ${on_string}: PathwayID2PathwayNames"/> | |
| 92 <data format="tabular" name="geneOutput" label="${tool.name} on ${on_string}: Gene KEGG Pathway File"> | |
| 93 <filter>(dataSets['whichDataSet'] == 'geneDataset') or (dataSets['whichDataSet'] == 'both')</filter> | |
| 94 </data> | |
| 95 <data format="tabular" name="metOutput" label="${tool.name} on ${on_string}: Metabolite KEGG Pathway File"> | |
| 96 <filter>(dataSets['whichDataSet'] == 'metDataset') or (dataSets['whichDataSet'] == 'both')</filter> | |
| 97 </data> | |
| 98 </outputs> | |
| 99 <tests> | |
| 100 <test> | |
| 101 <param name="species" value="rno"/> | |
| 102 <param name="whichDataSet" value="both"/> | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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103 <param name="geneKeggAnnot" value="gene_to_keggId_link.tsv"/> |
| 1 | 104 <param name="geneUniqId" value="UniqueID"/> |
| 105 <param name="geneName" value="GeneSymbol"/> | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
malex
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106 <param name="geneKeggId" value="KEGG_ID"/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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107 <param name="metKeggAnnot" value="metabolite_to_keggId_link.tsv"/> |
| 1 | 108 <param name="metUniqId" value="UniqueID"/> |
| 109 <param name="metName" value="MetName"/> | |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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110 <param name="metKeggId" value="KEGG_ID"/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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111 <output name="gene_keggID2pathID" file="geneKeggId2pathwayId.tsv" compare="diff" lines_diff="10000"/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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112 <output name="met_keggID2pathID" file="metaboliteKeggId2pathwayId.tsv" compare="diff" lines_diff="10000"/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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113 <output name="geneOutput" file="gene_kegg_pathway.tsv" compare="diff" lines_diff="10000"/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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114 <output name="metOutput" file="metabolite_kegg_pathway.tsv" compare="diff" lines_diff="10000"/> |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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115 <output name="pathways" file="pathwayId2pathwayNames.tsv" compare="diff" lines_diff="10000"/> |
| 1 | 116 </test> |
| 117 </tests> | |
| 118 <help><![CDATA[ | |
| 119 | |
| 120 **Tool Description** | |
| 121 | |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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122 This tool takes a Gene to KEGG Link dataset or a Metabolomic to KEGG Link dataset and adds KEGG Pathway Names using KEGGIDs. |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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123 The tool was designed to take the output from the 'Link Name to KEGGID' tool as input (for example the Gene to KEGGID Link dataset), |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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124 but other datasets containing KEGGIDs can be used as well. |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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125 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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126 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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127 If a 'Gene to KEGG ID link File’ is given, the tool outputs the following three files; |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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128 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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129 1) a 'Gene KEGG Pathway File' containing the unique FeatureID, Feature_Name, Feature_Type and KEGG_ID columns from the input file plus Pathway_ID and Pathway_Name columns containing KEGG pathway identifiers and KEGG pathway names, respectively. If no pathways are linked to the KEGG IDs then these columns return ‘NA’. |
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2c218a253d56
"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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130 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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131 2) a 'GeneKeggID2PathwayID' file containing the KEGG gene identifiers and their associated KEGG pathway identifiers. |
| 1 | 132 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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133 3) a 'PathwayID2PathwayNames' file containing all of the KEGG pathway identifiers and theirassociated KEGG pathway names. |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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134 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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135 If a 'Metabolite to KEGG ID link File’ is given, the tool outputs the following three files; |
| 1 | 136 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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137 1) a ' Metabolite KEGG Pathway File' containing the unique FeatureID, Feature_Name, Feature_Type and KEGG_ID columns from the input file plus Pathway_ID and Pathway_Name columns containing KEGG pathway identifiers and KEGG pathway names, respectively. If no pathways are linked to the KEGG IDs then these columns return ‘NA’. |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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138 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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139 2) a 'MetaboliteKeggID2PathwayID' file containing the KEGG metabolite identifiers and their associated KEGG pathway identifiers. |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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140 |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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141 3) a 'PathwayID2PathwayNames' file containing all of the KEGG pathway identifiers and their associated KEGG pathway names. |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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142 |
| 1 | 143 |
| 144 Note: FeatureIDs and KEGGIDs may not be unique in the output. | |
| 145 | |
| 146 -------------------------------------------------------------------------------- | |
| 147 | |
| 148 **INPUT** | |
| 149 | |
| 150 **Gene Dataset containing KEGGIDs - for example, output from the Link Name to KEGG IDtool** | |
| 151 | |
| 152 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ | |
| 153 | UniqueId | Gene_Name | Feature_Type | Matched | Name_in_KEGG | KEGGID | Similarity | Tie | Selected | | |
| 154 +==========+===========+==============+=========+==============+=========+============+=====+==========+ | |
| 155 | Gene_1 | one | Gene | Yes | one* | mmu:... | 1.0 | No | Yes | | |
| 156 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ | |
| 157 | Gene_2 | two | Gene | Yes | two* | mmu:... | 1.0 | No | Yes | | |
| 158 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ | |
| 159 | Gene_3 | three | Gene | Yes | three* | mmu:... | 1.0 | No | Yes | | |
| 160 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ | |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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161 | Gene_4 | four | Gene | No | NA | NA | NA | No | NA | |
| 1 | 162 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ |
| 163 | ... | ... | ... | ... | ... | ... | ... | ... | ... | | |
| 164 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ | |
| 165 | |
| 166 **Metabolite Dataset containing KEGGIDs - for example, output from the Link Name to KEGGID tool** | |
| 167 | |
| 168 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ | |
| 169 | UniqueId | Met_Name | Feature_Type | Matched | Name_in_KEGG | KEGGID | Similarity | Tie | Selected | | |
| 170 +==========+==========+==============+=========+==============+==========+============+=====+==========+ | |
| 171 | Met_1 | one | Metabolite | Yes | one* | cpd:... | 1.0 | No | Yes | | |
| 172 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ | |
| 173 | Met_2 | two | Metabolite | Yes | two* | cpd:... | 1.0 | No | Yes | | |
| 174 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ | |
| 175 | Met_3 | three | Metabolite | Yes | three* | cpd:... | 1.0 | No | Yes | | |
| 176 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ | |
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"planemo upload for repository https://github.com/secimTools/gait-gm/tree/main/galaxy commit 758394addb95b09e794132a23a1f7e95ba39df0b"
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177 | Met_4 | four | Metabolite | No | NA | NA | NA | No | NA | |
| 1 | 178 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ |
| 179 | ... | ... | ... | ... | ... | ... | ... | ... | ... | | |
| 180 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ | |
| 181 | |
| 182 **Gene unique FeatureID and/or Metabolite unique ID** | |
| 183 | |
| 184 Name of the column in your KEGGID Link File that contains unique identifiers (for genes and/or metabolites). | |
| 185 | |
| 186 **Gene Symbol** | |
| 187 | |
| 188 Name of the column in your KEGGID Link File that has Gene Symbols (for genes) or Metabolite Names (for metabolite data). | |
| 189 | |
| 190 **Gene KEGGID and/or Metabolite KEGGID** | |
| 191 | |
| 192 Name of the column in your KEGGID Link File that contains KEGGIDs (for genes and/or metabolites). | |
| 193 | |
| 194 -------------------------------------------------------------------------------- | |
| 195 | |
| 196 **OUTPUT** | |
| 197 | |
| 198 The user will get different output from the tool, depending on whether they include the 'Gene to KEGGID Link' File, the 'Metabolite to KEGGID Link' File, or both. | |
| 199 | |
| 200 (1) **GeneKeggID2PathwayID.** Downloaded file from KEGG for the selected species that contains ALL KEGGIDs to PathwayIDs. | |
| 201 (2) **MetaboliteKeggID2PathwayID.** Downloaded file from KEGG for the selected species that contains ALL the Metabolite KeggIDs to PathwayIDs. | |
| 202 (3) **Pathways Names.** Downloaded file from KEGG for the selected species that contains ALL the PathwayIDs to Pathway Names. | |
| 203 (4) **Gene KEGG Pathway File.** Tabular file with genes, feature types, KEGGIDs, PathwayIDs and Pathway Names. | |
| 204 | |
| 205 +-------------+--------------+--------------+---------+--------------+--------------+ | |
| 206 | FeatureID | Gene_Symbol | Feature_Type | KEGGID | PathwayID | Pathway_Name | | |
| 207 +=============+==============+==============+=========+==============+==============+ | |
| 208 | FeatureID_1 | one | Gene | mmu:... | path:mmu:... | Pathway_A | | |
| 209 +-------------+--------------+--------------+---------+--------------+--------------+ | |
| 210 | FeatureID_2 | two | Gene | mmu:... | path:mmu:... | Pathway_B | | |
| 211 +-------------+--------------+--------------+---------+--------------+--------------+ | |
| 212 | FeatureID_3 | three | Gene | mmu:... | path:mmu:... | Pathway_C | | |
| 213 +-------------+--------------+--------------+---------+--------------+--------------+ | |
| 214 | FeatureID_4 | four | Gene | mmu:... | path:mmu:... | Pathway_D | | |
| 215 +-------------+--------------+--------------+---------+--------------+--------------+ | |
| 216 | ... | ... | ... | ... | ... | ... | | |
| 217 +-------------+--------------+--------------+---------+--------------+--------------+ | |
| 218 | |
|
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219 ------------------------------------------------------------------ |
| 1 | 220 |
| 221 (5) **Metabolite KEGG Pathway File.** Tabular file with metabolites, feature types, KEGGIDs, PathwayIDs and Pathway Names. | |
| 222 | |
| 223 +-------------+-----------------+--------------+---------+--------------+--------------+ | |
| 224 | FeatureID | Metabolite_Name | Feature_Type | KEGGID | PathwayID | Pathway_Name | | |
| 225 +=============+=================+==============+=========+==============+==============+ | |
| 226 | FeatureID_1 | one | Metabolite | cdp:... | path:map:... | Pathway_A | | |
| 227 +-------------+-----------------+--------------+---------+--------------+--------------+ | |
| 228 | FeatureID_2 | two | Metabolite | cdp:... | path:map:... | Pathway_B | | |
| 229 +-------------+-----------------+--------------+---------+--------------+--------------+ | |
| 230 | FeatureID_3 | three | Metabolite | cdp:... | path:map:... | Pathway_C | | |
| 231 +-------------+-----------------+--------------+---------+--------------+--------------+ | |
| 232 | FeatureID_4 | four | Metabolite | cdp:... | path:map:... | Pathway_D | | |
| 233 +-------------+-----------------+--------------+---------+--------------+--------------+ | |
| 234 | ... | ... | ... | ... | ... | ... | | |
| 235 +-------------+-----------------+--------------+---------+--------------+--------------+ | |
| 236 | |
| 237 ]]> | |
| 238 </help> | |
| 239 <citations> | |
| 240 <citation type="bibtex">@ARTICLE{Kirpich17secimtools, | |
| 241 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre}, | |
| 242 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools}, | |
| 243 journal = {BMC Bioinformatics}, | |
|
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244 year = {2018} |
| 1 | 245 }</citation> |
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246 <citation type="bibtex">@article{Mor2021GaitGM, |
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247 title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease}, |
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248 author={Mor, DE and Huertas, F and Morse, AM and Kaletsky, R and Murphy, CT and Kalia, V and Miller, GW and Moskalenko, O and Conesa, A and McIntyre, LM}, |
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249 journal={BMC Genomics}, |
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250 year={submitted}, |
| 1 | 251 }</citation> |
| 252 </citations> | |
| 253 </tool> |