view STACKS_sort_read_pairs.xml @ 1:ccfa8e539bdf

add archive toolbox to manage zip outputs

<tool id="STACKSassembleperead" name="STACKS : assemble read pairs by locus" version="1.1.1">
  <description>Run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</description>

<requirements>
    <requirement type="package" version="1.18">stacks</requirement>
    <requirement type="package" version="1.2.10">velvet</requirement>
  </requirements>
<command interpreter="python">

STACKS_sort_read_pairs.py
-a $STACKS_archive
-e $samples_archive
#if str( $options_whitelist.whitelist_selector) == "yes"
-b $whitelist
#end if
#if str( $options_filter.reads_selector) == "yes"
-c $options_filter.threshold
#end if
#if str( $options_filter2.length_selector) == "yes"
-d $options_filter2.threshold2
#end if
-o $output


</command>

<inputs>
<param name="STACKS_archive" format="zip,tar.gz" type="data" label="Archive from STACKS pipeline regrouping all outputs" />

<param name="samples_archive" format="zip,fastq.gz,tar.gz,tar.bz2" type="data" label="Archive with raw reads used to execute previous STACKS pipeline" />

        <conditional name="options_whitelist">
<param name="whitelist_selector" type="select" label="Have you got a whitelist?" >
<option value="no" selected="true">No</option>
<option value="yes">Yes</option>
</param>
<when value="no"></when>
<when value="yes">
<param name="whitelist" format="txt, tabular" type="data" label="Whitelist file containing loci that we want to assemble: those that have SNPs" />
</when>
</conditional>


<conditional name="options_filter">
<param name="reads_selector" type="select" label="Specify a treshold for the minimum number of reads by locus?" >
<option value="no" selected="true">No</option>
<option value="yes">Yes</option>
</param>
<when value="no"></when>
<when value="yes">
<param name="threshold" type="integer" value="10" label="Minimum number of reads by locus"/>
</when>
</conditional>
<conditional name="options_filter2">
<param name="length_selector" type="select" label="Specify a minimum length for asssembled contigs?" >
<option value="no" selected="true">No</option>
<option value="yes">Yes</option>
</param>
<when value="no"></when>
<when value="yes">
<param name="threshold2" type="integer" value="200" label="Minimum length for asssembled contigs"/>
</when>
</conditional>

</inputs>
<outputs>
    <data format="fasta" name="output" label="collated.fa : ${tool.name} on ${on_string}" />
</outputs>
<stdio>
   <exit_code range="1" level="fatal" description="Error" />
</stdio> 
<help>

.. class:: infomark

**What it does**

This program will run each of the Stacks sort_read_pairs.pl and exec_velvet.pl utilities to assemble pair-end reads from STACKS pipeline results

--------

**Created by:**

Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko

--------

**Example:**

Input file:

Output archives of STACKS : Reference map or STACKS : De novo map, in zip or tar.gz format


Output file:

A collated.fa file containing assembled contigs for each locus


Instructions to add the functionality of archives management in Galaxy on the `eBiogenouest HUB wiki &lt;https://www.e-biogenouest.org/wiki/ManArchiveGalaxy&gt;`_ .

--------


**Project links:**

`STACKS website &lt;http://creskolab.uoregon.edu/stacks/&gt;`_ .

`STACKS manual &lt;http://creskolab.uoregon.edu/stacks/stacks_manual.pdf&gt;`_ .

`STACKS google group &lt;https://groups.google.com/forum/#!forum/stacks-users&gt;`_ .

--------

**References:**

-J. Catchen, P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. Stacks: an analysis tool set for population genomics. Molecular Ecology. 2013.

-J. Catchen, S. Bassham, T. Wilson, M. Currey, C. O'Brien, Q. Yeates, and W. Cresko. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Molecular Ecology. 2013.

-J. Catchen, A. Amores, P. Hohenlohe, W. Cresko, and J. Postlethwait. Stacks: building and genotyping loci de novo from short-read sequences. G3: Genes, Genomes, Genetics, 1:171-182, 2011.

-A. Amores, J. Catchen, A. Ferrara, Q. Fontenot and J. Postlethwait. Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication. Genetics, 188:799'808, 2011.

-P. Hohenlohe, S. Amish, J. Catchen, F. Allendorf, G. Luikart. RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow trout and westslope cutthroat trout. Molecular Ecology Resources, 11(s1):117-122, 2011.

-K. Emerson, C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, C. Holzapfel. Resolving postglacial phylogeography using high-throughput sequencing. Proceedings of the National Academy of Science, 107(37):16196-200, 2010.

--------

**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">10.1111/mec.12354</citation>
    <citation type="doi">10.1111/mec.12330</citation>
    <citation type="doi">10.1534/g3.111.000240</citation>
    <citation type="doi">10.1534/genetics.111.127324</citation>
    <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>
    <citation type="doi">10.1073/pnas.1006538107</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>