view renumber.xml @ 2:c8e16c8eff98 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 6944305517dcccad3e6b37f8aba0b43ccb004540

<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.webapollo.renumber" name="WA2: Renumber Genes" version="1.1">
  <description>following standard conventions</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/renumber.py

@AUTH@

@CN_OR_GUESS@

--prefix $prefix
--leading $leading
--email $__user_email__

> $output]]></command>
  <inputs>
    <expand macro="cn_or_guess" />
    <param name="prefix" type="text" label="Prefix" optional="True" value="gene_"/>
    <param name="leading" type="integer" value="3" label="Number of Leading Zeroes" />
  </inputs>
  <outputs>
    <data format="json" name="output"/>
  </outputs>
  <help><![CDATA[
**NOTA BENE**

All organism data is currently shared. By using this tool your annotation data will be visible to your fellow lab members.
This will be fixed at a later date.

This only works with JBrowse v0.4 and above!

**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.

@REFERENCES@
      ]]></help>
</tool>