view lordec_graph.xml @ 7:529da747c89c draft

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<tool id="lordecgraph" name="lordec_graph" version="0.6">
  <description>is an efficient tool to generate de Bruijn graph from PacBio corrected reads</description>
  <requirements>
    <requirement type="package" version="0.6">lordec</requirement>
  </requirements>
  <command><![CDATA[
lordec-build-SR-graph
-2 $short_reads
-k $kmer_len
-s $solid_threshold
-g $outgraph
#if str( $advanced_options.advanced_options_selector) == "advanced"
-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="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 graph advanced options">
<option value="default" selected="true">Default</option>
<option value="advanced">Advanced</option>
</param>
<when value="default"></when>
<when value="advanced">
<param name="threads" type="integer" label="number of threads" value="1" />
</when>
</conditional>

  </inputs>

  <outputs>
      <data format="HDF5"  name="outgraph" label="${tool.name} on ${on_string}: de_Bruijn_graph" />
  </outputs>
  <help>

**Description**
To correct long reads or to generate k-mer statistics, LoRDEC builds a de Bruijn Graph from the short reads file. This program allows to build and save the graph in a file before doing such analyses, and then to load the graph file instead of computing it from the short read file. This saves time if you reuse the graph several times. The graph is saved in [[http://fr.wikipedia.org/wiki/Hierarchical_Data_Format][Hierarchical Data Format]] (HDF5: version 5).


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)

[e-mail]

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>