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comparison add_kegg_pathway_info.xml @ 2:2c218a253d56 draft default tip

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"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
comparison
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1:ec9ee8edb84d 2:2c218a253d56
26 #if $dataSets.whichDataSet == "both": 26 #if $dataSets.whichDataSet == "both":
27 -gka=$dataSets.geneKeggAnnot 27 -gka=$dataSets.geneKeggAnnot
28 -gid=$dataSets.geneUniqId 28 -gid=$dataSets.geneUniqId
29 -gn=$dataSets.geneName 29 -gn=$dataSets.geneName
30 -gkid=$dataSets.geneKeggId 30 -gkid=$dataSets.geneKeggId
31 -go=$geneOutput
32 -kg2p=$gene_keggID2pathID
33 -mka=$dataSets.metKeggAnnot 31 -mka=$dataSets.metKeggAnnot
34 -mid=$dataSets.metUniqId 32 -mid=$dataSets.metUniqId
35 -mn=$dataSets.metName 33 -mn=$dataSets.metName
36 -mkid=$dataSets.metKeggId 34 -mkid=$dataSets.metKeggId
35 -kg2p=$gene_keggID2pathID
36 -km2p=$met_keggID2pathID
37 -go=$geneOutput
37 -mo=$metOutput 38 -mo=$metOutput
38 -km2p=$met_keggID2pathID
39 #end if 39 #end if
40 -p=$pathways 40 -p=$pathways
41 ]]></command> 41 ]]></command>
42 <inputs> 42 <inputs>
43 <param name="species" type="select" label="Select your Species from the List" > 43 <param name="species" type="select" label="Select your Species from the List" >
46 <option value="rno">Rattus norvegicus</option> 46 <option value="rno">Rattus norvegicus</option>
47 <option value="dme">Drosophila melanogaster</option> 47 <option value="dme">Drosophila melanogaster</option>
48 <option value="ath">Arabidopsis thaliana</option> 48 <option value="ath">Arabidopsis thaliana</option>
49 <option value="sce">Saccharomyces cerevisiae</option> 49 <option value="sce">Saccharomyces cerevisiae</option>
50 <option value="eco">Escherichia coli</option> 50 <option value="eco">Escherichia coli</option>
51 <option value="cel">Caenorhabditis elegans</option>
51 </param> 52 </param>
52 <conditional name="dataSets"> 53 <conditional name="dataSets">
53 <param name="whichDataSet" type="select" display="radio" label="Select the Datasets you want to add KEGG pathway information to. Note: datasets must contain KEGGIDs."> 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.">
54 <option value="both" selected="true">Gene Expression + Metabolomic Files with KEGGIDs</option> 55 <option value="both" selected="true">Gene Expression + Metabolomic Files with KEGGIDs</option>
55 <option value="geneDataset">Gene Expression File with KEGGIDs</option> 56 <option value="geneDataset">Gene Expression File with KEGGIDs</option>
56 <option value="metDataset">Metabolomic File with KEGGIDs</option> 57 <option value="metDataset">Metabolomic File with KEGGIDs</option>
57 <validator type="no_options" message="You must select at least one option." /> 58 <validator type="no_options" message="You must select at least one option." />
58 </param> 59 </param>
59 <when value="both"> 60 <when value="both">
60 <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"/> 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"/>
61 <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."/> 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."/>
62 <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."/> 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."/>
63 <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."/> 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."/>
64 <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"/> 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"/>
65 <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."/> 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."/>
66 <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."/> 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."/>
67 <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."/> 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."/>
68 </when> 69 </when>
69 <when value="geneDataset"> 70 <when value="geneDataset">
70 <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"/> 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"/>
71 <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."/> 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."/>
72 <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."/> 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."/>
73 <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."/> 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."/>
74 </when> 75 </when>
75 <when value="metDataset"> 76 <when value="metDataset">
76 <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"/> 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"/>
77 <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."/> 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."/>
78 <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."/> 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."/>
97 </outputs> 98 </outputs>
98 <tests> 99 <tests>
99 <test> 100 <test>
100 <param name="species" value="rno"/> 101 <param name="species" value="rno"/>
101 <param name="whichDataSet" value="both"/> 102 <param name="whichDataSet" value="both"/>
102 <param name="geneKeggAnnot" value="gene_to_keggId_link_01fhl.tsv"/> 103 <param name="geneKeggAnnot" value="gene_to_keggId_link.tsv"/>
103 <param name="geneUniqId" value="UniqueID"/> 104 <param name="geneUniqId" value="UniqueID"/>
104 <param name="geneName" value="GeneSymbol"/> 105 <param name="geneName" value="GeneSymbol"/>
105 <param name="geneKeggId" value="KEGGID"/> 106 <param name="geneKeggId" value="KEGG_ID"/>
106 <param name="metKeggAnnot" value="metabolite_to_keggId_link_01fhl.tsv"/> 107 <param name="metKeggAnnot" value="metabolite_to_keggId_link.tsv"/>
107 <param name="metUniqId" value="UniqueID"/> 108 <param name="metUniqId" value="UniqueID"/>
108 <param name="metName" value="MetName"/> 109 <param name="metName" value="MetName"/>
109 <param name="metKeggId" value="KEGGID"/> 110 <param name="metKeggId" value="KEGG_ID"/>
110 <output name="kgen2pathway" file="KGEN2PATHWAY"/> 111 <output name="gene_keggID2pathID" file="geneKeggId2pathwayId.tsv" compare="diff" lines_diff="10000"/>
111 <output name="kmet2pathway" file="KMET2PATHWAY"/> 112 <output name="met_keggID2pathID" file="metaboliteKeggId2pathwayId.tsv" compare="diff" lines_diff="10000"/>
112 <output name="pathways" file="PATHWAYS"/> 113 <output name="geneOutput" file="gene_kegg_pathway.tsv" compare="diff" lines_diff="10000"/>
113 <output name="output" file="kegg_downloader_table"/> 114 <output name="metOutput" file="metabolite_kegg_pathway.tsv" compare="diff" lines_diff="10000"/>
115 <output name="pathways" file="pathwayId2pathwayNames.tsv" compare="diff" lines_diff="10000"/>
114 </test> 116 </test>
115 </tests> 117 </tests>
116 <help><![CDATA[ 118 <help><![CDATA[
117 119
118 **Tool Description** 120 **Tool Description**
119 121
120 This tool takes a Gene to KEGG Link dataset, a Metabolomic to KEGG Link dataset or both and adds KEGG Pathway Names using KEGGIDs. 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) but other datasets containing KEGGIDs can be used as well. 122 This tool takes a Gene to KEGG Link dataset or a Metabolomic to KEGG Link dataset and adds KEGG Pathway Names using KEGGIDs.
121 123 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),
122 The user will get different outputs from the 'Add KEGG Pathway Info Tool', depending on the input. If a Gene to KEGGID Link dataset is given as input the tool outputs the following three files: 1) a Gene KEGG Pathway dataset containing the FeatureID, Feature_Name, Feature_Type and KEGGID columns from the input file and KEGG_PathwayIDs and KEGG Pathway Names from KEGG, 2) a GeneKeggID2PathwayID dataset containing all gene KEGGIDs in KEGG and their associated pathway KEGGIDs and 3) a PathwayID2PathwayNames dataset containing all of the pathway KEGGIDs and their associated KEGG pathway names. 124 but other datasets containing KEGGIDs can be used as well.
123 125
124 Analoguous files are generated by the tool if a Metabolite to KEGGID Link dataset is input by the user. 126
127 If a 'Gene to KEGG ID link File’ is given, the tool outputs the following three files;
128
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’.
130
131 2) a 'GeneKeggID2PathwayID' file containing the KEGG gene identifiers and their associated KEGG pathway identifiers.
132
133 3) a 'PathwayID2PathwayNames' file containing all of the KEGG pathway identifiers and theirassociated KEGG pathway names.
134
135 If a 'Metabolite to KEGG ID link File’ is given, the tool outputs the following three files;
136
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’.
138
139 2) a 'MetaboliteKeggID2PathwayID' file containing the KEGG metabolite identifiers and their associated KEGG pathway identifiers.
140
141 3) a 'PathwayID2PathwayNames' file containing all of the KEGG pathway identifiers and their associated KEGG pathway names.
142
125 143
126 Note: FeatureIDs and KEGGIDs may not be unique in the output. 144 Note: FeatureIDs and KEGGIDs may not be unique in the output.
127 145
128 -------------------------------------------------------------------------------- 146 --------------------------------------------------------------------------------
129 147
138 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ 156 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+
139 | Gene_2 | two | Gene | Yes | two* | mmu:... | 1.0 | No | Yes | 157 | Gene_2 | two | Gene | Yes | two* | mmu:... | 1.0 | No | Yes |
140 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ 158 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+
141 | Gene_3 | three | Gene | Yes | three* | mmu:... | 1.0 | No | Yes | 159 | Gene_3 | three | Gene | Yes | three* | mmu:... | 1.0 | No | Yes |
142 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ 160 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+
143 | Gene_4 | four | Gene | No | NA | NA | NA | Na | NA | 161 | Gene_4 | four | Gene | No | NA | NA | NA | No | NA |
144 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ 162 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+
145 | ... | ... | ... | ... | ... | ... | ... | ... | ... | 163 | ... | ... | ... | ... | ... | ... | ... | ... | ... |
146 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+ 164 +----------+-----------+--------------+---------+--------------+---------+------------+-----+----------+
147 165
148 **Metabolite Dataset containing KEGGIDs - for example, output from the Link Name to KEGGID tool** 166 **Metabolite Dataset containing KEGGIDs - for example, output from the Link Name to KEGGID tool**
154 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ 172 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+
155 | Met_2 | two | Metabolite | Yes | two* | cpd:... | 1.0 | No | Yes | 173 | Met_2 | two | Metabolite | Yes | two* | cpd:... | 1.0 | No | Yes |
156 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ 174 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+
157 | Met_3 | three | Metabolite | Yes | three* | cpd:... | 1.0 | No | Yes | 175 | Met_3 | three | Metabolite | Yes | three* | cpd:... | 1.0 | No | Yes |
158 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ 176 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+
159 | Met_4 | four | Metabolite | No | NA | NA | NA | Na | NA | 177 | Met_4 | four | Metabolite | No | NA | NA | NA | No | NA |
160 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ 178 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+
161 | ... | ... | ... | ... | ... | ... | ... | ... | ... | 179 | ... | ... | ... | ... | ... | ... | ... | ... | ... |
162 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+ 180 +----------+----------+--------------+---------+--------------+----------+------------+-----+----------+
163 181
164 **Gene unique FeatureID and/or Metabolite unique ID** 182 **Gene unique FeatureID and/or Metabolite unique ID**
196 | FeatureID_4 | four | Gene | mmu:... | path:mmu:... | Pathway_D | 214 | FeatureID_4 | four | Gene | mmu:... | path:mmu:... | Pathway_D |
197 +-------------+--------------+--------------+---------+--------------+--------------+ 215 +-------------+--------------+--------------+---------+--------------+--------------+
198 | ... | ... | ... | ... | ... | ... | 216 | ... | ... | ... | ... | ... | ... |
199 +-------------+--------------+--------------+---------+--------------+--------------+ 217 +-------------+--------------+--------------+---------+--------------+--------------+
200 218
201 219 ------------------------------------------------------------------
202 220
203 (5) **Metabolite KEGG Pathway File.** Tabular file with metabolites, feature types, KEGGIDs, PathwayIDs and Pathway Names. 221 (5) **Metabolite KEGG Pathway File.** Tabular file with metabolites, feature types, KEGGIDs, PathwayIDs and Pathway Names.
204 222
205 +-------------+-----------------+--------------+---------+--------------+--------------+ 223 +-------------+-----------------+--------------+---------+--------------+--------------+
206 | FeatureID | Metabolite_Name | Feature_Type | KEGGID | PathwayID | Pathway_Name | 224 | FeatureID | Metabolite_Name | Feature_Type | KEGGID | PathwayID | Pathway_Name |
221 <citations> 239 <citations>
222 <citation type="bibtex">@ARTICLE{Kirpich17secimtools, 240 <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
223 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre}, 241 author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
224 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools}, 242 title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
225 journal = {BMC Bioinformatics}, 243 journal = {BMC Bioinformatics},
226 year = {in press} 244 year = {2018}
227 }</citation> 245 }</citation>
228 <citation type="bibtex">@article{garcia2010paintomics, 246 <citation type="bibtex">@article{Mor2021GaitGM,
229 title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data}, 247 title={GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease},
230 author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana}, 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},
231 journal={Bioinformatics}, 249 journal={BMC Genomics},
232 volume={27}, 250 year={submitted},
233 number={1},
234 pages={137--139},
235 year={2010},
236 publisher={Oxford University Press}
237 }</citation> 251 }</citation>
238 </citations> 252 </citations>
239 </tool> 253 </tool>