Mercurial > repos > proteore > proteore_maps_visualization
changeset 5:f4e02d20546b draft
planemo upload commit c6b2e31fccac66c2caa687b375cbf9947f7ba88e-dirty
| author | proteore |
|---|---|
| date | Tue, 14 May 2019 09:28:50 -0400 |
| parents | 4cc2265d1294 |
| children | 005221a20848 |
| files | kegg_maps_visualization.R kegg_maps_visualization.xml |
| diffstat | 2 files changed, 21 insertions(+), 7 deletions(-) [+] |
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--- a/kegg_maps_visualization.R Thu Jan 31 05:19:10 2019 -0500 +++ b/kegg_maps_visualization.R Tue May 14 09:28:50 2019 -0400 @@ -75,6 +75,7 @@ } get_list_from_cp <-function(list){ + list = gsub(";","\t",list) list = gsub(",","\t",list) list = strsplit(list, "[ \t\n]+")[[1]] list = list[list != ""] #remove empty entry
--- a/kegg_maps_visualization.xml Thu Jan 31 05:19:10 2019 -0500 +++ b/kegg_maps_visualization.xml Tue May 14 09:28:50 2019 -0400 @@ -1,5 +1,5 @@ -<tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2019.01.31"> - <description>of (differentially expressed) genes/proteins</description> +<tool id="kegg_maps_visualization" name="Pathways visualization" version="2019.05.14"> + <description>of (differentially expressed) genes/proteins [KEGG]</description> <requirements> <requirement type="package" version="1.18.0">bioconductor-pathview</requirement> <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement> @@ -69,12 +69,15 @@ <add source=" " target=""/> </mapping> </sanitizer> + <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator> </param> </when> <when value="pathways_file"> <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol2" type="text" value="c1" label="Column of pathways IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> </when> </conditional> </when> @@ -103,12 +106,15 @@ <add source=" " target=""/> </mapping> </sanitizer> + <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator> </param> </when> <when value="pathways_file"> <param name="file" type="data" format="txt,tabular" label="Enter your file" help="Pathway id format : 'path:mmu00053' or 'mmu00053' or '00053'" /> <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> </when> </conditional> </when> @@ -137,12 +143,15 @@ <add source=" " target=""/> </mapping> </sanitizer> + <validator type="regex" message="Please enter correct pathway id(s)">([a-z]{3}[0-9]{5}[\s]*)+</validator> </param> </when> <when value="pathways_file"> <param name="file" type="data" format="txt,tabular" label="Select your file" help="Pathway id format : 'path:hsa00010' or 'hsa00010' or '00010'" /> <param name="header2" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' /> + <param name="ncol2" type="text" value="c1" label="Column of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> </when> </conditional> </when> @@ -174,11 +183,15 @@ <when value="file" > <param name="file" type="data" format="txt,tabular" label="Select your file" help="" /> <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol" type="text" value="c1" label="Column if 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="ncol" type="text" value="c1" label="Column if 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'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> <conditional name="foldchange" > <param name="fc" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Map quantitative data on the pathway?"/> <when value="true"> - <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4"/> + <param name="fc_col" type="text" label="Column(s) number of quantitative data (separated by ','. 3 columns max)" help="For example : c1,c3,c4"> + <validator type="regex" message="Please enter column numbers, for example: 'c1,c3' for first and third columns">([c]{0,1}[0-9]+[,]*){1,3}</validator> + </param> </when> <when value="false"/> </conditional>