# HG changeset patch # User drosofff # Date 1434792861 14400 # Node ID 8fe1c798372d8e462fb64a418b4e6776bb83bf8d # Parent 118834adb4ce0040aed57b7a5334d86bf820b96b planemo upload for repository https://bitbucket.org/drosofff/gedtools/ diff -r 118834adb4ce -r 8fe1c798372d cap3.xml --- a/cap3.xml Mon Jun 08 07:55:57 2015 -0400 +++ b/cap3.xml Sat Jun 20 05:34:21 2015 -0400 @@ -1,10 +1,11 @@ - + Sequence Assembly tool cap3 cap3 "$inputSequences" > "$cap3stdout"; + cat "$inputSequences".cap.contigs "$inputSequences".cap.singlets > $contigsandsinglets mv "$inputSequences".cap.contigs $contigs; mv "$inputSequences".cap.contigs.qual $contigsqual; mv "$inputSequences".cap.contigs.links $contigslink; @@ -19,16 +20,65 @@ - + + + + + + + + + + + + + + + + +**What it does** + +This tool is a CAP3 wrapper developed for the visitor2 set of worflows + +Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences + +Standard CAP3 outputs (Standard Output, Contigs Qual, Contigs Link, Ace and Info) are kept hidden in the Galaxy history (feel free to reveal these hidden datasets). + +Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets) + +**Acknowledgments** + +This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson the galaxy tool `get_fasta_from_taxon`_. + +It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_. + +.. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3 +.. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en +.. _MIT license: http://opensource.org/licenses/MIT + + + @article{Huang:1999wb, + author = {Huang, X and Madan, A}, + title = {{CAP3: A DNA sequence assembly program.}}, + journal = {Genome research}, + year = {1999}, + volume = {9}, + number = {9}, + pages = {868--877}, + month = sep + } + + + diff -r 118834adb4ce -r 8fe1c798372d test-data/ace.txt diff -r 118834adb4ce -r 8fe1c798372d test-data/cap3stdout.txt diff -r 118834adb4ce -r 8fe1c798372d test-data/contigs.fa diff -r 118834adb4ce -r 8fe1c798372d test-data/contigsandsinglets.fa diff -r 118834adb4ce -r 8fe1c798372d test-data/contigslink.txt diff -r 118834adb4ce -r 8fe1c798372d test-data/contigsqual.txt diff -r 118834adb4ce -r 8fe1c798372d test-data/singlets.fa