Mercurial > repos > proteore > proteore_prot_features
changeset 8:aca66c3b8fbb draft
planemo upload commit 3e8aad84b7fe9218370364b1aef3ea5779475f9f-dirty
| author | proteore |
|---|---|
| date | Fri, 10 May 2019 03:59:23 -0400 |
| parents | 69c70e45d5ab |
| children | 2eb72be62446 |
| files | add_protein_features.R add_protein_features.xml proteore_nextprot_ref.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 11 insertions(+), 8 deletions(-) [+] |
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--- a/add_protein_features.R Mon Mar 11 04:48:52 2019 -0400 +++ b/add_protein_features.R Fri May 10 03:59:23 2019 -0400 @@ -194,7 +194,7 @@ res = res[!duplicated(res$NextprotID),] output_content = merge(file, res,by.x=ncol,by.y="NextprotID",incomparables = NA,all.x=T) output_content = order_columns(output_content,ncol,id_type,file) - output_content = output_content[,-which(colnames(output_content)=="NextprotID")] #remove nextprotID column + if (id_type=="Uniprot_AC"){output_content = output_content[,-which(colnames(output_content)=="NextprotID")]} #remove nextprotID column output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x))) #convert "" et " " to NA write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE) }
--- a/add_protein_features.xml Mon Mar 11 04:48:52 2019 -0400 +++ b/add_protein_features.xml Fri May 10 03:59:23 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="prot_features" name="Add protein features" version="2019.03.11"> +<tool id="prot_features" name="Add protein features" version="2019.05.10"> <description>[neXtProt] </description> <requirements> @@ -24,7 +24,7 @@ --diseases_info='$Nextprot_params.diseases_info' --output='$output' - #if 'nextprot_ref' in str($ref_file).split("/") + #if 'proteore_nextprot_ref' in str($ref_file).split("/") --nextprot="$ref_file" #else --nextprot="$__tool_directory__/$ref_file" @@ -81,11 +81,13 @@ <option value="SubcellLocations" selected="false">Subcellular Location</option> </param> - <param name="diseases_info" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Disease information" /> + <param name="diseases_info" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Disease information" /> </section> <param name="ref_file" type="select" label="Release of neXtProt reference file to use"> - <options from_data_table="proteore_nextprot_ref"/> + <options from_data_table="proteore_nextprot_ref"> + <filter type="sort_by" column="1"/> + </options> </param> </inputs>
--- a/proteore_nextprot_ref.loc.sample Mon Mar 11 04:48:52 2019 -0400 +++ b/proteore_nextprot_ref.loc.sample Fri May 10 03:59:23 2019 -0400 @@ -1,2 +1,3 @@ -#<id> <name> <value> -nextprot_ref_09-03-2019 neXtProt release 09-03-2019 tool-data/nextprot_ref_09-03-2019.tsv +#<id> <release> <name> <value> +9979818992 nextprot_ref_08-10-2018 neXtProt release 08-10-2018 tool-data/nextprot_ref_08-10-2018.tsv +9979809691 nextprot_ref_09-03-2019 neXtProt release 09-03-2019 tool-data/nextprot_ref_09-03-2019.tsv
--- a/tool_data_table_conf.xml.sample Mon Mar 11 04:48:52 2019 -0400 +++ b/tool_data_table_conf.xml.sample Fri May 10 03:59:23 2019 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tables> <table name='proteore_nextprot_ref' comment_char="#"> - <columns>id, name, value</columns> + <columns>id, release, name, value</columns> <file path="tool-data/proteore_nextprot_ref.loc"/> </table> </tables>