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+++ b/add_kegg_anno_info.xml	Fri Jun 18 20:23:19 2021 +0000
@@ -0,0 +1,219 @@
+<tool id="secimtools_add_kegg_anno_info" name="Link Name to KEGGID" version="@WRAPPER_VERSION@">
+  <description></description>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <stdio> 
+    <exit_code range="1" level="fatal" description="Repeated Unique IDs"/> 
+  </stdio> 
+  <command detect_errors="exit_code"><![CDATA[
+  add_kegg_anno_info.py
+    -s=$species
+    #if $dataSets.whichDataSet == "geneDataset":
+      -ga=$dataSets.geneAnnot
+      -gid=$dataSets.geneUniqId
+      -gn=$dataSets.geneName
+    #end if
+    #if $dataSets.whichDataSet == "metDataset":
+      -ma=$dataSets.metAnnot
+      -mid=$dataSets.metUniqId
+      -mn=$dataSets.metName
+    #end if
+    #if $dataSets.whichDataSet == "geneDataset,metDataset":
+      -ga=$dataSets.geneAnnot
+      -gid=$dataSets.geneUniqId
+      -gn=$dataSets.geneName
+      -ma=$dataSets.metAnnot
+      -mid=$dataSets.metUniqId
+      -mn=$dataSets.metName
+    #end if
+    -go=$geneOutput
+    -mo=$metOutput
+  ]]></command>
+  <inputs>
+    <param name="species" type="select" label="Select Species from the list" >
+     <option value="hsa">Homo sapiens</option>
+     <option value="mmu">Mus musculus</option>
+     <option value="rno">Rattus norvegicus</option>
+     <option value="dme">Drosophila melanogaster</option>
+     <option value="ath">Arabidopsis thaliana</option>
+     <option value="sce">Saccharomyces cerevisiae</option>
+     <option value="eco">Escherichia coli</option>
+    </param>
+    <conditional name="dataSets">
+      <param name="whichDataSet" type="select" display="radio" label="Select Annotation Dataset(s)">
+        <option value="geneDataset,metDataset" selected="true">Gene Expression + Metabolomic Annotation Datasets</option>
+        <option value="geneDataset">Gene Expression Annotation Dataset</option> 
+        <option value="metDataset">Metabolomic Annotation Dataset</option>
+        <validator type="no_options" message="You must select at least one option." /> 
+      </param>
+      <when value="geneDataset">
+        <param name="geneAnnot" type="data" format="tabular" label="Select the Gene Expression Annotation dataset from your History"/>
+        <param name="geneUniqId" type="text" size="30" value="" label="Gene Unique FeatureID" help="Name of the column in your Gene Expression Annotation dataset that contains the unique FeatureIDs."/> 
+        <param name="geneName" type="text" size="30" value="" label="Gene Symbol" help="Name of the column in your Gene Expression Annotation dataset that contains Gene Symbols to use for linking to KEGGIDs."/> 
+      </when>
+      <when value="metDataset">
+        <param name="metAnnot" type="data" format="tabular" label="Select the Metabolomic Annotation dataset from your History" />
+        <param name="metUniqId" type="text" size="30" value="" label="Metabolite Unique FeatureID" help="Name of the column in your Metabolomic Annotation dataset that contains the unique FeatureIDs."/>
+        <param name="metName" type="text" size="30" value="" label="Metabolite Names" help="Name of the column in your Metabolomic Annotation dataset that has metabolite names to use for linking to KEGGIDs."/>
+      </when>
+      <when value="geneDataset,metDataset">
+        <param name="geneAnnot" type="data" format="tabular" label="Select the Gene Expression Annotation dataset from your History"/>
+        <param name="geneUniqId" type="text" size="30" value="" label="Gene Unique FeatureID" help="Name of the column in your Gene Expression Annotation dataset that contains the unique FeatureIDs."/> 
+        <param name="geneName" type="text" size="30" value="" label="Gene Symbol" help="Name of the Column in your Gene Expression Annotation dataset that contains Gene Symbols to use for linking to KEGGIDs."/> 
+        <param name="metAnnot" type="data" format="tabular" label="Select the Metabolomic Annotation dataset from your History" />
+        <param name="metUniqId" type="text" size="30" value="" label="Metabolite Unique FeatureID" help="Name of the Column in your Metabolomic Annotation dataset that contains the unique FeatureIDs."/> 
+        <param name="metName" type="text" size="30" value="" label="Metabolite Names" help="Name of the Column in your Metabolomic Annotation dataset that has metabolite names to use for linking to KEGGIDs."/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="geneOutput" label="${tool.name} on ${on_string}: Gene to KEGGID link">
+      <filter>(dataSets['whichDataSet'] == 'geneDataset') or (dataSets['whichDataSet'] == 'geneDataset,metDataset')</filter>
+    </data>
+    <data format="tabular" name="metOutput" label="${tool.name} on ${on_string}: Metabolite to KEGGID link">
+      <filter>(dataSets['whichDataSet'] == 'metDataset') or (dataSets['whichDataSet'] == 'geneDataset,metDataset')</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="species" value="rno"/>
+      <param name="geneAnnot" value="ensembl2symbol_annotation_file_01fhl.tsv"/>
+      <param name="geneUniqId" value="UniqueID"/>
+      <param name="geneName" value="GeneSymbol"/>
+      <param name="metAnnot" value="metabolite_annotation_file_01fhl.tsv"/>
+      <param name="metUniqId" value="UniqueID"/>
+      <param name="metName" value="MetName"/>
+      <param name="geneOutput" value="gene_link_kegg_annotation_file_01fhl.tsv"/>
+      <param name="metOutput" value="metabolite_link_kegg_annotation_file_01fhl.tsv"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+
+**Tool Description**
+
+  This tool takes an annotation dataset containing metabolite compound names or gene symbols and links them to identifiers in KEGG (KEGGIDs) 
+  creating either a (a) Gene to KEGGID Link or  a (b) Metabolite to KEGGID Link dataset. For gene expression data, the tool is designed to 
+  take the output from the 'Map ENSEMBLIDs to Gene Symbols' tool as input. If your input dataset contains a Selected column, the tool will 
+  link GeneSymbols to KEGGIDs where Selected = 'Yes'. Input Files without a Selected column must have a column containing unique FeatureIDs. 
+  This tool takes an annotation dataset containing unique FeatureIDs, ENSEMBLIDs (for gene expression data) and GeneSymbol/MetaboliteName 
+  and adds the following columns:  1) Name_in_KEGG, the name found in KEGG, 2) Matched, a column indicating whether a match was found in KEGG, 
+  3) KEGGID, the KEGG identifier for the Match, 4) Score, a similarity score representing match similarity (caluclated using the python internal 
+  function SequenceMatcher from difflib (check) and 5) a Tie column to indicate if a gene symbol or metabolite name matched more than one KEGGID.
+
+  User-specified metabolite names are linked to KEGGIDs by identifying the best match using the following procedure.  Common metabolite prefixes 
+  are removed (cis-, trans-, d- , l- , (s)-, alpha-, beta-, alpha, beta, alpha-d-, beta-d-, alpha-l-, beta-l-, l-beta-, l-alpha-, d-beta-, d-alpha-).  
+  If the metabolite name given is an acid, then the name is modified to the conjugate base by replacing  “ic acid”, “icacid” or “ic_acid” with  “ate”.  
+  If amino acids are given in 1-letter or 3-letter abbreviations, names are modified to the full amino acid name.  The following commonly used lipid 
+  abbreviations are modified to reflect the full names (SM = sphingomyelin, lysopc  = lysophosphatidylcholine, PC = phosphatidylcholine, 
+  PE = phosphatidylethanolamine and LysoPE = lysophosphatidylethanolamine).  Similarly, abbreviations for other commonly assayed metabolites are 
+  modified to reflect the full names (cit = citrate, orn = ornithine, thyr = thyroxine and boc = butoxycarbonyl). The code allows the addition of 
+  more synonyms. The user-specified metabolite names are retained in the output dataset for comparisons with the KEGG database.
+ 
+  Each parsed metabolite name is compared to metabolite names in KEGG. The best match in KEGG based on similarity score is returned.  The similarity 
+  score (Score column) is based on the longest contiguous matching subsequence that does not contain 'junk' elements where 'junk' elements are defined 
+  as duplicates making up more than 1% of a sequence with minimum length of 200 (python SequenceMatcher class from difflib)
+
+  Selected = Yes for the match with the highest similarity score.  
+
+  For metabolite names where the best match is tied with at least one other compound in KEGG, all matches are returned. A tie is determined as follows:  
+  if the Score is greater than 95% for 2 or more matches in the metabolite name then:
+  1) the Tie column = 'Yes' and a warning message will appear
+  2) the Selected column is sorted alphabetically on the Name_in_KEGG column. Note that the user-specified FeatureID and MetaboliteName may not be unique in the resulting output dataset.
+
+--------------------------------------------------------------------------------
+
+**INPUT**
+
+**Annotation File**
+
+  +-------------+--------------+-----+
+  | FeatureID   | Name         | ... |
+  +=============+==============+=====+
+  | FeatureID_1 | one          | ... |
+  +-------------+--------------+-----+
+  | FeatureID_2 | two          | ... |
+  +-------------+--------------+-----+
+  | FeatureID_3 | three        | ... |
+  +-------------+--------------+-----+
+  | FeatureID_4 | four         | ... |
+  +-------------+--------------+-----+
+  | ...         | ...          | ... |
+  +-------------+--------------+-----+
+
+    **NOTE:** This dataset must contain at least two columns, a column of FeatureIDs and a column containing names (e.g. gene symbol or compound names) to use for linking to KEGGIDs. Other columns may be present in the dataset. The user can use a Gene Expression Annotation dataset, a Metabolomic Annotation dataset or both.
+
+**Unique FeatureID**
+
+  Name of the column in your gene expression or metabolomic Annotation dataset that contains the Unique FeatureIDs.
+
+**Gene Symbol or Metabolite Names**
+
+  Name of the column in your gene expression or metabolomic Annotation dataset with the names to use for matching to KEGGIDs.
+
+--------------------------------------------------------------------------------
+
+**OUTPUT**
+
+For each input Annotation file, a TSV file containing the following columns is generated:
+
+  (1) **unique FeatureID:**  column from the Annotation dataset containing the unique FeatureIDs.
+  (2) **Name:**  column from Annotation dataset used for matching in KEGG.
+  (3) **Feature_Type:**  column indicating whether matching was for metabolites or genes.
+  (4) **Matched:**  column indicating whether a match in KEGG was found.  Yes/No
+  (5) **Name_in_KEGG:**  column containing the KEGG name for the match.
+  (6) **KEGGID:**  column containing the KEGG identifier for the match.
+  (7) **Similarity:**  value indicating the similarity between the given feature and the match in KEGG.  Ranges from 0 to 1.
+  (8) **Tie:**  in cases where multiple matches are found for a given feature, Tie = yes if the similarity is greater than 95%. 
+  (9) **Selected:**  for features with multiple matches and different similarity scores, the 'Selected' column = yes for the match with the highest similarity score. For features with multiple	matches and the same similarity score, the 'Selected' column = yes based on the alphabetical order of the returned match.
+
+
+**Example Metabolite to KEGGID Link Table**
+
+  +-------------+------------+--------------+---------+--------------+----------+------------+-----+----------+
+  | FeatureID   | Name       | Feature_Type | Matched | Name_in_KEGG | KEGG_ID  | Similarity | Tie | Selected |
+  +=============+============+==============+=========+==============+==========+============+=====+==========+
+  | FeatureID_1 | one        | Metabolite   | Yes     | one*         | cpd:...  | 1.0        | No  | Yes      |
+  +-------------+------------+--------------+---------+--------------+----------+------------+-----+----------+
+  | FeatureID_2 | two        | Metabolite   | Yes     | two*         | cpd:...  | 1.0        | No  | Yes      |
+  +-------------+------------+--------------+---------+--------------+----------+------------+-----+----------+
+  | FeatureID_3 | two        | Metabolite   | Yes     | three*       | cpd:...  | 0.87       | No  | No       |
+  +-------------+------------+--------------+---------+--------------+----------+------------+-----+----------+
+  | FeatureID_4 | four       | Metabolite   | No      | NA           | NA       | NA         | NA  | NA       |
+  +-------------+------------+--------------+---------+--------------+----------+------------+-----+----------+
+  | ...         | ...        | ...          | ...     | ...          | ...      | ...        | ... | ...      |
+  +-------------+------------+--------------+---------+--------------+----------+------------+-----+----------+
+
+    **NOTE:** Warning messages appear in cases of a Tie (greater than 95% similarity). Please check these results carefully.
+
+  ]]>
+  </help>
+  <citations>
+    <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
+    author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+    title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+    journal = {BMC Bioinformatics},
+    year = {in press}
+    }</citation>
+    <citation type="bibtex">
+    @article{garcia2010paintomics,
+    title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+    author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+    journal={Bioinformatics},
+    volume={27},
+    number={1},
+    pages={137--139},
+    year={2010},
+    publisher={Oxford University Press}
+    }</citation>
+    <citation>@article{wu2014mygene,
+    title={MyGene. info: gene annotation query as a service},
+    author={Wu, Chunlei and Mark, Adam and Su, Andrew I},
+    journal={bioRxiv},
+    pages={009332},
+    year={2014},
+    publisher={Cold Spring Harbor Laboratory}
+    }</citation>
+  </citations>
+</tool>