Mercurial > repos > gga > apollo_create_or_update
diff create_or_update_organism.xml @ 0:cd595b5d890a 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 05:46:00 -0400 |
parents | |
children | b194ffbd6ae1 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_or_update_organism.xml Mon Sep 11 05:46:00 2017 -0400 @@ -0,0 +1,75 @@ +<?xml version="1.0"?> +<tool id="create_or_update" name="Create or Update Organism" version="3.2"> + <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>