Mercurial > repos > earlhaminst > ensembl_get_feature_info
diff get_feature_info/get_feature_info.xml @ 0:874c067e4527 draft
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/Ensembl-REST commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
author | earlhaminst |
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date | Thu, 11 Aug 2016 14:29:29 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_feature_info/get_feature_info.xml Thu Aug 11 14:29:29 2016 -0400 @@ -0,0 +1,55 @@ +<tool id="get_feature_info" name="Get Ensembl features by ID" version="0.1.1"> + <description>using REST API</description> + <requirements> + <requirement type="package" version="2.7">requests</requirement> + </requirements> + <command> +<![CDATA[ +python $__tool_directory__/get_feature_info.py +-e $expand +-f $format_selector +-i "$input" +-s $species_selector +> "$output" +]]> + </command> + + <inputs> + <param name="input" type="data" format="txt" label="List of Ensembl IDs" help="Max 1000 IDs" /> + <param name="species_selector" type="select" label="Select Species"> + <option value="ensembl" selected="true">Vertebrates</option> + <option value="ensemblgenomes">Other species</option> + </param> + <param name="expand" type="boolean" truevalue="1" falsevalue="0" label="Expand the search to include any connected features" help="For example, if the object is a gene, its transcripts, translations and exons will be returned as well" /> + <param name="format_selector" type="select" label="Output format"> + <option value="full" selected="true">Full</option> + <option value="condensed">Condensed</option> + </param> + </inputs> + + <outputs> + <data name="output" format="json" label="$(tool.name) on ${on_string}" /> + </outputs> + + <tests> + <test> + <param name="input" ftype="txt" value="input.txt" /> + <param name="expand" value="false" /> + <output name="outputFile" file="out.json" /> + </test> + </tests> + + <help> +<![CDATA[ +**What it does** + +Retrieve feature information in JSON format from Ensembl using its REST API. + +Uses the `"POST lookup/id"`_ API endpoint. + +.. _"POST lookup/id": http://rest.ensembl.org/documentation/info/lookup_post +]]> + </help> + <citations> + </citations> +</tool>