view bootstrap.xml @ 7:b6ece07bec6a draft

planemo upload commit 45906ba522c7c319067e93d5cd5d7161223c3336

<tool id="PHYLO_bootstrap" name="Prepare data" version="1.1.0">
  <description>for analysis</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package">yapp_env</requirement>
  </requirements>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <version_command>echo "bootstrap script 1.1.0"</version_command>
  <command interpreter="bash">
    bootstrap-wrapper.sh $config
  </command>
  <inputs>
    <param name="plate_id" type="integer" value="1" label="Plate number"/>
    <conditional name="run_type">
      <param name="run_type_select" type="select" label="Run type">
        <option value="junior">Junior</option>
        <option value="senior">Senior</option>
      </param>
      <when value="junior"></when>
      <when value="senior">
        <param name="zone_id" type="integer" value="1" label="Zone number"/>
      </when>
    </conditional>
    <param name="sample_info" type="data" format="csv" label="Sample information"/>
  </inputs>
  <outputs>
    <data format="csv" name="barcodes" label="Specimen-to-barcode map"/>
    <data format="csv" name="labels" label="Specimen-to-label map"/>
    <data format="csv" name="metadata" label="Metadata template"/>
  </outputs>
  <configfiles>
    <configfile name="config">
PLATE_ID="${plate_id}"
#if $run_type.run_type_select == "senior"
JUNIOR=""
ZONE_ID="${run_type.zone_id}"
#else
JUNIOR="--junior"
ZONE_ID="1"
#end if
SAMPLE_INFO="${sample_info}"

BARCODES="${barcodes}"
LABELS="${labels}"
METADATA="${metadata}"
    </configfile>
  </configfiles>
  <!-- The contents of the help tag is parsed as reStructuredText. Please see
       help-template.rst for examples of commonly-used sections in other Galaxy
       tools. -->
  <help>

.. class:: infomark

**What it does**

This tool parses sample information and creates a mapping of samples to
barcodes. The sample information file must contain the columns ``sampleid``,
``barcode``, and ``reverse``, and can optionally contain a ``zone`` column
also.

  </help>
</tool>