Mercurial > repos > gga > apollo_create_or_update
view create_or_update_organism.xml @ 4:aee984715db1 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
author | gga |
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date | Mon, 12 Mar 2018 06:32:08 -0400 |
parents | b194ffbd6ae1 |
children | 696a1962212e |
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<?xml version="1.0"?> <tool id="create_or_update" name="Create or Update Organism" version="3.3"> <description>will create the organism if it doesn't exist, and update otherwise</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <code file="webapollo.py"/> <command detect_errors="aggressive"><![CDATA[ cp -R '${jbrowse.extra_files_path}/data/' "@DATA_DIR@/${jbrowse.id}" && python $__tool_directory__/create_or_update_organism.py @ADMIN_AUTH@ --genus '$genus' --species '$species' #if str($group) != "None": --group '${group}' #end if ${remove_old_directory} $public @ORG_OR_GUESS@ "@DATA_DIR@/${jbrowse.id}" $__user_email__ > $output]]></command> <inputs> <param name="jbrowse" type="data" format="html" label="JBrowse HTML Output" /> <expand macro="org_or_guess" /> <param name="genus" type="text" label="Genus" optional="False" /> <param name="species" type="text" label="Species" optional="True" /> <param name="public" type="boolean" truevalue="--public" falsevalue="" label="Is Organism Public" /> <param name="group" type="select" dynamic_options="galaxy_list_groups(__trans__)" label="Grant access to a user group" optional="True" /> <param name="remove_old_directory" type="boolean" truevalue="--remove_old_directory" falsevalue="" label="Remove old data directory" /> </inputs> <outputs> <data format="json" name="output"/> </outputs> <tests> <test expect_failure="true"> <param name="jbrowse" value="good-model.gff3"/> <conditional name="org_source"> <param name="source_select" value="direct"/> <param name="org_raw" value="Test org" /> </conditional> <param name="genus" value="genus"/> <assert_stderr> <has_text text="cannot stat" /> </assert_stderr> </test> </tests> <help><![CDATA[ **What it does** Adds an organism to the Apollo database. The tool takes the output of a JBrowse run as that contains all of the necessary information for which tracks are appropriate for a given analysis. **WARNINGS** - Do not use names which conflict with other users. - If you provide an Apollo JSON file, only the first organism block will be used in Common Name determination, as it is improbable you wish to apply a single JBrowse instance to multiple organisms. @REFERENCES@ ]]></help> <expand macro="citations"/> </tool>