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Commit message:
planemo upload commit 08f1831e097df5d74bf60ff5955e7e9c8e524cc8-dirty |
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modified:
README.rst goprofiles.xml |
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| diff -r 58a8ddd58dde -r ed226f0e5625 README.rst --- a/README.rst Wed Mar 07 09:08:44 2018 -0500 +++ b/README.rst Wed Mar 14 12:51:53 2018 -0400 |
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| @@ -15,7 +15,7 @@ ----------------------------------- -This tool, based on the goProfiles R package, performs statistical analysis of functional profiles. It is based on GO ontology and considers either a gene set ('Entrez’ Identifiers) or a protein set (Uniprot ID) as input. +This tool, based on the goProfiles R package, performs statistical analysis of functional profiles. It is based on GO ontology and considers either a gene set ('Entrez’ Identifiers) or a protein set (Uniprot accession number) as input. You can choose one or more GO categories: @@ -23,8 +23,8 @@ * Cellular Component (CC) * Molecular Function (MF) -Functional profile at a given GO level is obtained by counting the number of identifiers having a hit in each category of this level (2 by default). Results are displayed as bar plots (with absolute or relative frequencies) and can be exported in pdf, png and jpeg formats. +Functional profile at a given GO level is obtained by counting the number of identifiers having a hit in each category of this level (2 by default). Results are displayed as bar plots (with absolute or relative frequencies) and can be exported in pdf, png and jpeg formats; textual output with GO terms and their computed frequencies is also provided. For more details about GoProfiles, please read: Salicrú et al. Comparison of lists of genes based on functional profiles. BMC Bioinformatics. 2011;12:401.(https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-401) -If your type of identifiers is not supported (i.e. different form Uniprot and Entrez), please use the **ID Converter** component in the ProteoRE section to convert your list of IDs first. +If your type of identifiers is not supported (i.e. different from Uniprot and Entrez), please use the **ID Converter** tool in the ProteoRE section to convert your list of IDs first. |
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| diff -r 58a8ddd58dde -r ed226f0e5625 goprofiles.xml --- a/goprofiles.xml Wed Mar 07 09:08:44 2018 -0500 +++ b/goprofiles.xml Wed Mar 14 12:51:53 2018 -0400 |
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| @@ -64,7 +64,7 @@ </when> <when value="file" > <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> - <param name="ncol" type="text" label="The column number of IDs to use" 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="The column number of IDs to use" 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 contain header?" /> <param name="id_type" type="select" label="Please select the type of your IDs list" > <option value="Entrez">Entrez Gene ID</option> |