Mercurial > repos > eric-rasche > apollo
view delete_features.xml @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
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children | f9a6e151b3b4 |
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<?xml version="1.0"?> <tool id="edu.tamu.cpt2.webapollo.delete_features" name="Delete all annotations from an Apollo record" version="1.2"> <description></description> <macros> <import>macros.xml</import> </macros> <code file="webapollo.py"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ #if str($ask_one) == "yes": #if str($ask_two) == "yes": ## Nope, still don't trust them to not be dumb (or malicious), so we backup first. python $__tool_directory__/export.py @ADMIN_AUTH@ @ORG_OR_GUESS@ --gff "$gff_out" --fasta "$fasta_out" --json "$json_out"; ## Now we delete python $__tool_directory__/delete_features.py @ADMIN_AUTH@ @ORG_OR_GUESS@ "$__user_email__" > $output; #else echo "Nothing to do" > $output; #end if #else echo "Nothing to do" > $output; #end if ]]></command> <inputs> <expand macro="org_or_guess" /> <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/> <param name="ask_two" type="boolean" truevalue="yes" falsevalue="" label="Are you really, really SURE you want to do this?" help="There's NO coming back from this."/> </inputs> <outputs> <data format="tabular" name="output" label="Process and Error Log"/> <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/> <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/> <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/> </outputs> <help><![CDATA[ **What it does** Deletes every single one of the annotations on an organism. Intentionally. **Why?** There are legitimate uses for this tool, generally re-opened genomes is a good one. Needing to transfer annotations from one build of an organism to another (with the same refseq name). @REFERENCES@ ]]></help> </tool>