<tool id="lordeccorrect" name="lordeccorrect" version="0.6">
  <description>is an efficient tool for correcting sequencing errors in PacBio reads</description>
  <requirements>
    <requirement type="package" version="0.6">lordec</requirement>
  </requirements>
  <command><![CDATA[
lordec-correct
-2 $short_reads
-i $long_reads
-k $kmer_len
-o $corrected_read_file
-s $solid_threshold
-S $stat_file
#if str( $advanced_options.advanced_options_selector) == "advanced"
-t $advanced_options.trials
-b $advanced_options.branch
-e $advanced_options.errorrate
-T $advanced_options.threads
#end if
2>&1
]]>
  </command>

  <inputs>
<!-- Input data files -->
<param name="short_reads" type="data" format="fasta,fastq.gz,fastq" label="short read FASTA/Q file" />
<param name="long_reads" type="data" format="fasta,fastq.gz,fastq" label="long read FASTA/Q file" help="PacBio reads files" />
<param name="kmer_len" type="integer" label="Size of kmers" value="31" help="Only uneven number"/>
<param name="solid_threshold" type="integer" label="solidity abundance threshold for k-mers" value="4" />
<conditional name="advanced_options">
<param name="advanced_options_selector" type="select" label="lordec correct advanced options">
<option value="default" selected="true">Default</option>
<option value="advanced">Advanced</option>
</param>
<when value="default"></when>
<when value="advanced">
<param name="trials" type="integer" label="number of target k-mers" value="5" />
<param name="branch" type="integer" label="maximum number of branches to explore" value="200" />
<param name="errorrate" type="float" label="maximum error rate" value="0.4" />
<param name="threads" type="integer" label="number of threads" value="1" />
</when>
</conditional>

  </inputs>

  <outputs>
      <data format="fasta"  name="corrected_read_file" label="${tool.name} on ${on_string}: corrected_read_file.fa" />
      <data format="txt"  name="stat_file" label="${tool.name} on ${on_string}: stat_file" />
  </outputs>
  <help>

**Description**
Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina).

LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters.

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**Web site**

http://www.atgc-montpellier.fr/lordec/

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**Integrated by**

Yvan Le Bras and Cyril Monjeaud

GenOuest Bio-informatics Core Facility

UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)

support@genouest.org

If you use this tool in Galaxy, please cite :

`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_

  </help>
  <citations>
    <citation type="doi">10.1186/s13742-015-0105-2</citation>
    <citation type="doi">10.1093/bioinformatics/btu538</citation>
    <citation type="bibtex">@INPROCEEDINGS{JOBIM2013,
    author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
    title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
    booktitle = {JOBIM 2013 Proceedings},
    year = {2013},
    url = {https://www.e-biogenouest.org/resources/128},
    pages = {97-106}
    }</citation>
</citations>
</tool>