Mercurial > repos > eric-rasche > apollo
diff 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 |
parents | |
children | f9a6e151b3b4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/delete_features.xml Wed Mar 01 22:39:58 2017 -0500 @@ -0,0 +1,60 @@ +<?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> +