Mercurial > repos > proteore > proteore_pathview_mapping
changeset 8:33c9bd75882a draft
planemo upload commit 1953798eb28b6e45c78342ed4c6a6a978d096fca
| author | proteore |
|---|---|
| date | Thu, 30 Aug 2018 06:12:51 -0400 |
| parents | b617d4bbebf8 |
| children | 560541195c3f |
| files | PathView.R Pathview.xml README.rst |
| diffstat | 3 files changed, 59 insertions(+), 20 deletions(-) [+] |
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--- a/PathView.R Mon Aug 27 11:21:34 2018 -0400 +++ b/PathView.R Thu Aug 30 06:12:51 2018 -0400 @@ -56,6 +56,9 @@ --expression_values3 Column containing expression values (third condition) --native_kegg TRUE : native KEGG graph, FALSE : Graphviz graph --species KEGG species (hsa, mmu, ...) + --pathways_input Tab with pathways in a column, output format of find_pathways + --pathway_col Column of pathways to use + --header2 Boolean, TRUE if header FALSE if not Example: ./PathView.R --input 'input.csv' --pathway_id '05412' --id_type 'uniprotID' --id_column 'c1' --header TRUE \n\n") @@ -108,7 +111,14 @@ #load("/home/dchristiany/proteore_project/ProteoRE/tools/pathview/args.Rda") ###setting variables -if (!is.null(args$pathways_id)) { ids <- sapply(rapply(strsplit(clean_bad_character(args$pathways_id),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE)} +if (!is.null(args$pathways_id)) { + ids <- sapply(rapply(strsplit(clean_bad_character(args$pathways_id),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) +}else if (!is.null(args$pathways_input)){ + header2 <- str2bool(args$header2) + pathway_col <- as.numeric(gsub("c", "" ,args$pathway_col)) + pathways_file = read_file(args$pathways_input,header2) + ids <- sapply(rapply(strsplit(clean_bad_character(pathways_file[,pathway_col]),","),c), function(x) remove_kegg_prefix(x),USE.NAMES = FALSE) +} #if (!is.null(args$pathways_name)) {names <- as.vector(sapply(strsplit(args$pathways_name,","), function(x) concat_string(x),USE.NAMES = FALSE))} if (!is.null(args$id_list)) {id_list <- as.vector(strsplit(clean_bad_character(args$id_list),","))} id_type <- tolower(args$id_type) @@ -117,6 +127,10 @@ #output <- args$output native_kegg <- str2bool(args$native_kegg) species=args$species +#org list used in mapped2geneID +org <- c('Hs','Mm') +names(org) <- c('hsa','mmu') + #read input file or list @@ -140,7 +154,7 @@ if (id_type == "uniprotid") { uniprotID = tab[,ncol] - mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = "Hs", pkg.name = NULL) + mapped2geneID = id2eg(ids = uniprotID, category = "uniprot", org = org[[species]], pkg.name = NULL) geneID = mapped2geneID[,2] tab = cbind(tab,geneID) @@ -188,6 +202,8 @@ #####mapping geneID (with or without expression values) on KEGG pathway +plot.col.key=!is.null(tab$e1) #if there's no exrepession data, we don't show the color key + for (id in ids) { pathview(gene.data = mat, #gene.idtype = "geneID", @@ -217,6 +233,8 @@ #high = list(gene = "red", cpd = "yellow"), #na.col = "transparent", #sign.pos="bottomleft", + plot.col.key = plot.col.key, + #high = "lightgreen", #key.pos="topright", #new.signature=TRUE, #rankdir="LB",
--- a/Pathview.xml Mon Aug 27 11:21:34 2018 -0400 +++ b/Pathview.xml Thu Aug 30 06:12:51 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.27"> +<tool id="Pathview" name="KEGG pathway mapping (pathview)" version="2018.08.30"> <requirements> <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> </requirements> @@ -11,10 +11,12 @@ --id_column="$input.ncol" --header="$input.header" #end if - #if $species.pathways.pathways_id == "pathways_ids" + #if $species.pathways.pathways_id != "pathways_file" --pathways_id="$species.pathways.pids" #else - --pathways_id="$species.pathways.pids" + --pathways_input="$species.pathways.file" + --header2="$species.pathways.header2" + --pathway_col="$species.pathways.ncol2" #end if --id_type="$id_type" --native_kegg="$native" @@ -36,6 +38,10 @@ ]]></command> <inputs> + <param name="id_type" type="select" label="Select your identifiers type :"> + <option value="uniprotID">Uniprot Accession number</option> + <option value="geneID">Entrez gene ID</option> + </param> <conditional name="input" > <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list from a file (e.g. table)" > <option value="text">Copy/paste your identifiers</option> @@ -55,8 +61,8 @@ </when> <when value="file" > <param name="file" type="data" format="txt,tabular" label="Select a file that contains your list of IDs" help="" /> - <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> - <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> + <param name="ncol" type="text" value="c1" label="The column which contains your IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> <conditional name="expression_values"> <param name="nb_exp" type="select" label="How many expression values column in your file ?"> <option value="0" >0</option> @@ -81,11 +87,6 @@ </conditional> </when> </conditional> - <param name="id_type" type="select" label="select your identifiers type :"> - <option value="uniprotID">Uniprot Accession number</option> - <option value="geneID">Entrez gene ID</option> - </param> - <conditional name="species"> <param name="ref_file" type="select" label="Select species" > <option value="hsa">Human (hsa)</option> @@ -96,6 +97,7 @@ <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> <option value="pathways_names">KEGG pathway name(s)</option> <option value="pathways_ids">KEGG pathway id(s)</option> + <option value="pathways_file">KEGG pathway id(s) from file</option> </param> <when value="pathways_names"> <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> @@ -106,7 +108,7 @@ </param> </when> <when value="pathways_ids"> - <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'> + <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412" or "path:hsa00010"'> <sanitizer invalid_char=''> <valid initial="string.printable"> <remove value="'"/> @@ -117,6 +119,11 @@ </sanitizer> </param> </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contains a header?" /> + <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> </conditional> </when> <when value="mmu"> @@ -124,6 +131,7 @@ <param name="pathways_id" type="select" label="Provide your pathway(s)" help="Enter KEGG pathway name(s) or KEGG pathway id(s)"> <option value="pathways_names">KEGG pathway name(s)</option> <option value="pathways_ids">KEGG pathway id(s)</option> + <option value="pathways_file">KEGG pathway id(s) from file</option> </param> <when value="pathways_names"> <param name="pids" type="select" label="Select pathway(s)" multiple="true" help='You can select one or several pathway(s), you can write the beginning of your pathways to search using autocomplete'> @@ -134,7 +142,7 @@ </param> </when> <when value="pathways_ids"> - <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "00010,05412" or "hsa00010,hsa05412"'> + <param name="pids" type="text" label="Copy/paste your pathway id(s)" help='IDs must be separated by "," into the form field, for example: "path:mmu00053" or "mmu00053,mmu00340" or "00053"'> <sanitizer invalid_char=''> <valid initial="string.printable"> <remove value="'"/> @@ -145,6 +153,11 @@ </sanitizer> </param> </when> + <when value="pathways_file"> + <param name="file" type="data" format="txt,tabular" label="Select a file with a column of pathways id " help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" /> + <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> + <param name="ncol2" type="text" value="c1" label="The column which contains your pathways ids" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + </when> </conditional> </when> </conditional> @@ -194,13 +207,17 @@ <help><![CDATA[ This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. +Select your identifier type : UniprotAC or Entrez gene ID + Select an input file containing ids in a column, set header and column number or copy/paste your ids. -Select your identifier type and a species of interest (for now only human available). +You can import 1 to 3 column(s) of expression values if you are importing ids from a file. + +Select a species of interest. -Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) +Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) or import it from a file. -Select the graph format : KEGG or graphviz +Select the graph format : KEGG (jpg) or graphviz (pdf) Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways.
--- a/README.rst Mon Aug 27 11:21:34 2018 -0400 +++ b/README.rst Thu Aug 30 06:12:51 2018 -0400 @@ -15,13 +15,17 @@ This tool map a list of Uniprot Accession number or Entrez gene ID to KEGG pathway with pathview R package. +Select your identifier type : UniprotAC or Entrez gene ID + Select an input file containing ids in a column, set header and column number or copy/paste your ids. -Select your identifier type and a species of interest (for now only human available). +You can import 1 to 3 column(s) of expression values if you are importing ids from a file. + +Select a species of interest. -Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) +Select one or several pathways of interest from the dropdown menu or copy/paste KEGG pathway id(s) or import it from a file. -Select the graph format : KEGG or graphviz +Select the graph format : KEGG (jpg) or graphviz (pdf) Uniprot accession number converted to Entrez geneID or Entrez geneID are mapped to each selected pathways.