comparison tools/spades_2_5/spades.xml @ 7:95ddc2380130 draft

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6:1b1af74a54ae

<tool id="spades" name="spades" version="0.6">
  <description>SPAdes genome assembler for regular and single-cell projects</description>
  <requirements>
    <requirement type="package" version="2.5.1">spades</requirement>
  </requirements>
  <command interpreter="perl">spades.pl 

    ## Forces unzipped output, faster
    --disable-gzip-output
    $sc
    $onlyassembler
    $careful
    $rectangles
    -t $threads 
    -k $kmers 
    ##-i $iterations 
    ##--phred-offset
    ## Sequence files
    #for $i, $library in enumerate( $libraries )
      #set num=$i+1

      <option value="false">No</option>
      <option value="true">Yes</option>
    </param>
    <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
    <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." />
    <param name="rectangles" type="boolean" truevalue="--rectangles" falsevalue="" checked="False" label="Use rectangle graph algorithm for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental, use at your own risks)." />
    <param name="threads" type="integer" label="Number of threads to use" value="16">
    </param>
    <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1"> -->
    <!-- </param>     -->
    <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." >
    </param>
    <!-- Reads -->
    <repeat name="libraries" title="Libraries">
      <param name="lib_type" type="select" label="Library type">
	<option value="paired_end">Paired end / Single reads</option>
	<option value="mate_paired">Mate pairs</option>
      </param>
      <param name="orientation" type="select" label="Orientation">
	<option value="fr" selected="true">-> &lt;- (fr)</option>
	<option value="rf">&lt;- -> (rf)</option>
	<option value="ff">-> -> (ff)</option>
      </param>
      <repeat name="files" title="Files">
	<conditional name="file_type">
	  <param name="type" type="select" label="Select file format">
	    <option value="separate">Separate input files</option>
	    <option value="interleaved">Interleaved files</option>
	    <option value="unpaired">Unpaired/Single reads</option>

    <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
    <data name="out_log" format="txt" label="SPAdes log" />
  </outputs>
  <!--  <tests>
    <test>
      
      <param name="sc" value="false" />
      <param name="careful" value="false" />
      <param name="rectangle" value="false" />
      <param name="threads" value="16" />
      <param name="kmers" value="33,55" />
      <param name="type" value="pairedend" />
      <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
      <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
      <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />

This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.
  </help>
</tool>

7:95ddc2380130

<tool id="spades" name="spades" version="0.7">
  <description>SPAdes genome assembler for regular and single-cell projects</description>
  <requirements>
    <requirement type="package" version="2.5.1">spades</requirement>
  </requirements>
  <command interpreter="perl">spades.pl 

    ## Forces unzipped output, faster
    --disable-gzip-output
    $sc
    $onlyassembler
    $careful
    ##$rectangles
    -t \${GALAXY_SLOTS:-16}
    -k "$kmers"
    ##-i $iterations 
    ##--phred-offset
    ## Sequence files
    #for $i, $library in enumerate( $libraries )
      #set num=$i+1

      <option value="false">No</option>
      <option value="true">Yes</option>
    </param>
    <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" />
    <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." />
    <!-- <param name="rectangles" type="boolean" truevalue="- -rectangles" falsevalue="" checked="False" label="Use rectangle graph algorithm for repeat resolution?" help="Uses rectangle graph algorithm for repeat resolution stage instead of usual SPAdes repeat resolution module (experimental, use at your own risks)." /> It uses a different format for the sequence identifier in the output FASTA files which do not contain the coverage information -->
    <!-- <param name="iterations" type="integer" label="Number of iterations for read error correction." value="1" /> -->
    <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." >
    </param>
    <!-- Reads -->
    <repeat name="libraries" title="Libraries" min="1" help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided.">
      <param name="lib_type" type="select" label="Library type">
	<option value="paired_end">Paired-end / Single reads</option>
	<option value="mate_paired">Mate pairs</option>
      </param>
      <param name="orientation" type="select" label="Orientation">
	<option value="fr" selected="true">-> &lt;- (fr)</option>
	<option value="rf">&lt;- -> (rf)</option>
	<option value="ff">-> -> (ff)</option>
      </param>
      <repeat name="files" title="Files" min="1">
	<conditional name="file_type">
	  <param name="type" type="select" label="Select file format">
	    <option value="separate">Separate input files</option>
	    <option value="interleaved">Interleaved files</option>
	    <option value="unpaired">Unpaired/Single reads</option>

    <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
    <data name="out_log" format="txt" label="SPAdes log" />
  </outputs>
  <!--  <tests>
    <test>
      <param name="sc" value="false" />
      <param name="careful" value="false" />
      <param name="kmers" value="33,55" />
      <param name="type" value="pairedend" />
      <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
      <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
      <output name="out_contigs" file="reference_1K.fa" ftype="fasta" compare="re_match" lines_diff="1" />

This wrapper is copyrighted by Lionel Guy, and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program.  If not, see http://www.gnu.org/licenses/.

** Acknowledgments **

Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.

Nicola Soranzo fixed bugs in the 0.6 version.
  </help>
</tool>