comparison lordec_correct.xml @ 3:e978c66bb55f draft

Uploaded

2:2e8e1bf4febf

<tool id="lordeccorrect" name="lordeccorrect" version="0.5.3">
  <description>is an efficient tool for correcting sequencing errors in PacBio reads</description>
  <requirements>
    <requirement type="package" version="0.5.3">lordec</requirement>
  </requirements>
  <command>
lordec-correct
-2 $short_reads
-i $long_reads
-k $kmer_len
-o $corrected_read_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" />

-------

**Integrated by**

Yvan Le Bras and Cyril Monjeaud 

GenOuest Bio-informatics Core Facility

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

`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. <https://www.e-biogenouest.org/resources/128>`_

  </help>
  <citations>
    <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>

3:e978c66bb55f

<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

#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" />

-------

**Integrated by**

Yvan Le Bras and Cyril Monjeaud

GenOuest Bio-informatics Core Facility

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

`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. <https://www.e-biogenouest.org/resources/128>`_

  </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>