annotate mapsembler2.xml @ 2:5aea5b993ae8

fix .dat unknown extension for kissreads

<tool id="mapsembler2" name="Mapsembler2" version="2.2.3">
  <description>is a targeted assembly software.</description>
  <requirements>
    <requirement type="package" version="2.2.3">mapsembler2</requirement>
  </requirements>
<command interpreter="python">
mapsembler2.py
-s $input_starters
-r $data_files
-e $extension_format
-t $output_extension
-k $kmer
-c $coverage
-d $substitutions
-g $genome_size
-f $process_search
-x $max_length
-y $max_depth
--output $output
-i $index_files
</command>

  <inputs>
	<!-- Input data files -->
	<param name="input_starters" type="data" format="fasta" label="Starters" help="set of input sequences" /> 	
	<param name="data_files" type="data" multiple="true" format="fasta,fastq" label="Read file" help="Data loaded in the script" />
        <param name="extension_format" type="select" label="Input files">
               <option value="fasta">fasta</option>
               <option value="fastq">fastq</option>
        </param>
	<param name="output_extension" type="select" label="Select your output extension type">
		<option value="1">a strict sequence</option>
		<option value="2">a consensus sequence</option>
		<option value="3">a strict graph</option>
		<option value="4">a consensus graph</option>
	</param>
	<param name="kmer" type="integer" label="Size of kmers" value="31" help="Set the length of used kmers. Must fit the compiled value. Only uneven number" />
	<param name="coverage" type="integer" label="Minimal coverage" value="5" help="set the minimal coverage: Used by Phaser (don't use kmers with lower coverage) "/>
        <param name="substitutions" type="integer" label="Number of authorized substitutions" value="1" help="set the number of authorized substitutions used while mapping reads on finding SNPs"/>
	<param name="genome_size" type="integer" label="Estimated genome size" value="10000000" help="Used only to control memory usage. e.g.3 billion (3000000000) uses 4Gb of RAM." />
        <param name="process_search" type="select" label="Process of search" help="Set the process of search in the graph" >
		<option value="1">Breadth</option>
                <option value="2">Depth</option>
 	</param>
        <param name="max_length" type="integer" label="Max length of nodes" value="40" help="set the maximal length of nodes"/>
        <param name="max_depth" type="integer" label="Max depth of nodes" value="10000" help="set the maximal depth of the graph"/>
	<param name="index_files" type="boolean" checked="false" default="false" label="Include index output files" />
  </inputs>

  <outputs>
      <data format="txt" name="output" label="${tool.name} on ${on_string}: out.txt" >
		<discover_datasets pattern="__designation_and_ext__" directory="job_outputs" visible="true" />
      </data>

  </outputs>
  <stdio>
    <exit_code range="1" level="fatal" description="Error in Stacks Denovo execution" />
  </stdio>
  <help>

**Description**

Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-coherent starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice.
Mapsembler2 may be used for (not limited to):

· Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced.

· Checks if a gene (input as starter) has an homolog in a set of reads.

· Checks if a known enzyme is present in a metagenomic NGS read set.

· Enrich unmappable reads by extending them, possibly making them mappable.

· Checks what happens at the extremities of a contig.

· Remove contaminants or symbiont reads from a read set

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**Web site**

http://colibread.inria.fr/mapsembler2/

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**Integrated by**

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">10.1186/1471-2105-13-48</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>