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delete_organism.xml
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delete_organism.xml
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<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.webapollo.delete_organism" name="Delete an Apollo record" version="1.0">
<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 $__tool_directory__/delete_organism.py
@ADMIN_AUTH@
@ORG_OR_GUESS@
"$__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>