view create_or_update_organism.xml @ 5:7610987e0c48 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3

<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.webapollo.create_or_update" name="Create or Update Organism" version="3.1">
  <description>will create the organism if it doesn't exist, and update otherwise</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <code file="webapollo.py"/>
  <expand macro="requirements"/>
  <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"
--group '${group}'
$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" />
  </inputs>
  <outputs>
    <data format="json" name="output"/>
  </outputs>
  <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>
</tool>