Mercurial > repos > gga > apollo_feat_from_gff3
diff create_features_from_gff3.xml @ 0:5aa3bc8d0253 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
author | gga |
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date | Mon, 11 Sep 2017 05:45:37 -0400 |
parents | |
children | 7c4a3e737e08 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_features_from_gff3.xml Mon Sep 11 05:45:37 2017 -0400 @@ -0,0 +1,50 @@ +<?xml version="1.0"?> +<tool id="feat_from_gff3" name="GFF3 to Apollo Annotations" version="0.9"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <code file="webapollo.py"/> + <command detect_errors="aggressive"><![CDATA[ +python $__tool_directory__/create_features_from_gff3.py +@ADMIN_AUTH@ +@ORG_OR_GUESS@ + +"$__user_email__" +'$gff3_data' +--source "${__app__.config.galaxy_infrastructure_url}history/view/${__app__.security.encode_id($gff3_data.history_id)}" + +> $output]]></command> + <inputs> + <expand macro="org_or_guess" /> + <expand macro="gff3_input" /> + </inputs> + <outputs> + <data format="tabular" name="output" label="Process and Error Log"/> + </outputs> + <tests> + <test expect_failure="true"> + <conditional name="org_source"> + <param name="source_select" value="direct"/> + <param name="org_raw" value="Test org" /> + </conditional> + <param name="gff3_data" value="good-model.gff3"/> + <expand macro="test_result" /> + </test> + </tests> + <help><![CDATA[ +**NOTA BENE** + +This is **incredibly, highly experimental** + +DO NOT: + +- Run on gff3 referencing multiple reference sequences/contigs +- Expect it to work well +- Expect it to work at all + +@REFERENCES@ +]]></help> + <expand macro="citations"/> +</tool>