annotate create_or_update_organism.xml @ 5:696a1962212e draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2

<?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">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>
  </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>