<tool id="wade" name="Wade" version="0.2.5+galaxy1">
    <description>identify regions of interest</description>
    <requirements>
        <requirement type="package" version="0.2.5">wade</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[



        #if $mode.type == 'GAS':

          #for $i in $mode.input#
            cp '$i' '$i.element_identifier' &&
          #end for

          #set $samples = ','.join([$i.element_identifier for $i in ( $mode.input )])
          #set $subtype = $mode.subtype

        #else:

          #for $i in $mode.subtype_input.input#
            cp '$i' '$i.element_identifier' &&
          #end for

          #set $samples = ','.join([$i.element_identifier for $i in ( $mode.subtype_input.input )])
          #set $subtype = $mode.subtype_input.subtype

        #end if

        Rscript --vanilla -e 'library(wade); source(file = system.file("exec/wade_cmd.R", package = "wade"))'

        -d 'output'

        -o '$mode.type'

        -t '$subtype'

        -s '$samples'

    ]]></command>
    <inputs>
    <conditional name="mode">
      <param name="type" type="select" label="Analysis Group">
        <option value="GAS">Streptococcus pyogenes</option>
        <option value="GONO">Streptococcus pneumoniae</option>
        <option value="PNEUMO">Neisseria gonorrhoeae</option>
      </param>
      <when value="GAS">
        <param name="subtype" type="select" label="Select specific analysis">
          <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
          <option value="EMM">EMM Typing</option>
          <option value="MLST">MLST Type</option>
          <option value="VFDB">VFDB (Virulence Factor Database)</option>
          <option value="MASTER">AMR/Toxin/Virulence Profiler</option>
        </param>
        <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
      </when>
      <when value="GONO">

        <conditional name="subtype_input">
        <param name="subtype" type="select" label="Select specific analysis">
          <option value="MLST">MLST Type</option>
          <option value="NGMAST">NG-MAST Type</option>
          <option value="NGSTAR">NG-STAR Type</option>
          <option value="rRNA23S">23S rRNA Alleles</option>
          <option value="MASTER">AMR/NG-STAR Profiler</option>
        </param>
        <when value="rRNA23S">
          <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
        </when>
        <when value="MLST">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        <when value="NGMAST">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        <when value="NGSTAR">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        <when value="MASTER">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        </conditional>

      </when>
      <when value="PNEUMO">

        <conditional name="subtype_input">
        <param name="subtype" type="select" label="Select specific analysis">
          <option value="AMR">ARG-ANNOT/Resfinder/CARD</option>
          <option value="MLST">MLST Type</option>
          <option value="VFDB">VFDB (Virulence Factor Database)</option>
          <option value="rRNA23S">23S rRNA Alleles</option>
          <option value="MASTER">AMR/Virulence Profiler</option>
        </param>
        <when value="rRNA23S">
          <param name="input" type="data" format="vcf" multiple="true" label="VCF file(s)"/>
        </when>
        <when value="AMR">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        <when value="MLST">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        <when value="VFDB">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        <when value="MASTER">
          <param name="input" type="data" format="fasta" multiple="true" label="Contig Fasta file(s)"/>
        </when>
        </conditional>

      </when>
    </conditional>
    </inputs>
    <outputs>
      <data name="report" format="csv">
        <discover_datasets pattern="__designation_and_ext__" directory="output" visible="true" />
      </data>
    </outputs>
    <tests>
        <test>
          <param name="input" value="SC19-2806-A.fasta"/>
          <output name='report'>
            <discovered_dataset designation="GAS_dbpipeline_WADE">
              <assert_contents>
                <has_text text="SampleNo" />
              </assert_contents>
            </discovered_dataset>
          </output>
        </test>
    </tests>
    <help><![CDATA[
==============
Wade
==============

R Script to generate results

=====
Legal 
=====

Copyright Government of Canada 2019

Written by: National Microbiology Laboratory, Public Health Agency of Canada

Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this work except in compliance with the License. You may obtain a copy of the
License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed
under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
CONDITIONS OF ANY KIND, either express or implied. See the License for the
specific language governing permissions and limitations under the License.

=======
Contact
=======

**Gary van Domselaar**: gary.vandomselaar@canada.ca

    ]]></help>
    <citations>
        <citation type="bibtex">@ARTICLE{a1,
            title = {R Script to generate results.},
            author = {Adrian Zetner},
            url = {https://github.com/phac-nml/wade}
            }
        }</citation>
    </citations>
</tool>