| Next changeset 1:029e38c5063a (2017-01-23) |
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gblocks.xml |
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| diff -r 000000000000 -r 56329c936868 gblocks.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gblocks.xml Mon Jan 23 07:39:23 2017 -0500 |
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| @@ -0,0 +1,112 @@ +<tool id="gblocks" name="Gblocks" version="0.91.1"> + <description>cleaning aligned sequences</description> + <edam_operations> + <edam_operation>operation_0368</edam_operation> + </edam_operations> + <requirements> + <requirement type="package" version="0.91b">gblocks</requirement> + </requirements> + <command> + ln -s ${input} input.fasta; + Gblocks + input.fasta + #if not 'default' in $b1: + -b1=$b1 + #end if + #if not 'default' in $b2: + -b2=$b2 + #end if + -b3=$b3 + -b4=$b4 + -b5=$b5 + + $datatype + + > $gblocks_log; + mv input.fasta-gb $output_aln; + mv input.fasta-gb.htm $output_htm; + + </command> + <inputs> + <param name="input" type="data" format="fasta" label="Source file" help="Fasta format"/> + <param name="datatype" type="select" label="Data type"> + <option value="-t=d">DNA</option> + <option value="-t=c">Codon</option> + <option value="-t=p">Protein</option> + </param> + <param name="b1" type="text" value="default" label="Minimum number of sequences for a conserved position, must be BIGGER than half the number" help="By default, = 50% of the number of sequences +1." /> + <param name="b2" type="text" value="default" label="Minimum number of Sequences for a flank position, SMALLER than Minimum Number Of Sequences For A Conserved Position" help="By default, = 85% of the number of sequences"/> + + <param name="b3" type="integer" value="8" label="Maximum number of contiguous non-conserved positions" help="All segment with contiguous non-conserved positions bigger than this value is rejected" /> + <param name="b4" type="integer" value="10" label="Minimum length of a block" help="Any integer >1" /> + <param name="b5" type="select" label="Allowed gap positions"> + <option value="n">None</option> + <option value="h">With half</option> + <option value="a">All</option> + </param> + <param name="display_gblocks_log" type="boolean" checked="False" label="Display gblocks standard output" /> + </inputs> + <outputs> + <data format="text" name="gblocks_log" label="Gblocks log: ${input.name}" > + <filter>display_gblocks_log == True</filter> + </data> + <data format="fasta" name="output_aln" label="Gblocks Cleaned sequencies: ${input.name}" /> + <data format="html" name="output_htm" label="Gblocks Sequencies information: ${input.name}" /> + </outputs> + <tests> + <test> + <param name="input" value="nad3.pir"/> + <param name="output_aln" value="nad3.pir-gb"/> + <param name="output_htm" value="nad3.pir-gb.htm"/> + </test> + </tests> + <help> + +.. class:: infomark + +**GBlocks version 0.91b, 2000** + +----- + +============== + Please cite: +============== + +"Improvement_ of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments." + + +.. _Improvement: http://sysbio.oxfordjournals.org/content/56/4/564.full + +**Talavera G., and Castresana J.** + +Systematic Biology 56, 564-577, 2007. + + +"Selection_ of conserved blocks from multiple alignments for their use in phylogenetic analysis." + + +.. _Selection: http://mbe.oxfordjournals.org/content/17/4/540 + +**Castresana J.** + +Molecular Biology and Evolution 17, 540-552, 2000. + +----- + +========== + Overview +========== + +Gblocks is a computer program written in ANSI C language that eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. These positions may not be homologous or may have been saturated by multiple substitutions and it is convenient to eliminate them prior to phylogenetic analysis. Gblocks selects blocks in a similar way as it is usually done by hand but following a reproducible set of conditions. The selected blocks must fulfill certain requirements with respect to the lack of large segments of contiguous nonconserved positions, lack of gap positions and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. Gblocks outputs several files to visualize the selected blocks. + +The use of a program such as Gblocks reduces the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible and, finally, facilitates the reproduction of the alignments and subsequent phylogenetic analysis by other researchers. Gblocks is very fast in processing alignments and it is therefore highly suitable for large-scale phylogenetic analyses. Several parameters can be modified to make the selection of blocks more or less stringent. In general, a relaxed selection of blocks is better for short alignments, whereas a stringent selection is more adequate for longer ones. Be aware that the default options of Gblocks are stringent. + +----- + +For further informations, please visite the Gblocks_ website. + + +.. _Gblocks: http://molevol.cmima.csic.es/castresana/Gblocks.html + </help> + +</tool> |