Mercurial > repos > dcorreia > bmge
changeset 11:a943abb980db draft default tip
planemo upload commit e0ca504b3313992020acf8ab7aed0a261237766e-dirty
| author | dcorreia |
|---|---|
| date | Mon, 06 Feb 2017 09:06:14 -0500 |
| parents | c348ec5aebcc |
| children | |
| files | BMGE.xml bmge/bmge.xml bmge/tool_dependencies.xml tool_dependencies.xml |
| diffstat | 4 files changed, 144 insertions(+), 144 deletions(-) [+] |
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--- a/BMGE.xml Wed Dec 21 07:54:36 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,138 +0,0 @@ -<tool id="bmge" name="BMGE" version="1.12"> - <description>cleaning aligned sequences</description> - <edam_operations> - <edam_operation>operation_2089</edam_operation> - </edam_operations> - <requirements> - <requirement type="package" version="1.12">BMGE</requirement> - </requirements> - <command>BMGE -i $input - -t $dataType.codeSeq - -m $dataType.matrice$dataType.estimated - -w $windowsSize - -g $rateCutOff - -h $entropy_threshold - -b $minBlock - #for $output in $outputFormat.value - #if $output - -$output file$output - #end if - #end for - </command> - - <inputs> - <param name="input" format="fasta" type="data" label="Source file" help="Fasta format"/> - <conditional name="dataType"> - <param name="codeSeq" type="select" label="Sequence Coding"> - <option value="DNA">DNA</option> - <option value="AA">AA</option> - <option value="CODON">Codon</option> - </param> - <when value="DNA"> - <param name="matrice" type="hidden" label="matrice" value="DNAPAM"/> - <param name="estimated" type="integer" label="Name of the PAM matrix [ 1-500 ]" value="250" min="1" max="500"/> - </when> - <when value="AA"> - <param name="matrice" type="hidden" label="matrice" value="BLOSUM"/> - <param name="estimated" type="select" label="Estimated matrice BLOSUM"> - <option value="30">30</option> - <option value="35">35</option> - <option value="40">40</option> - <option value="45">45</option> - <option value="50">50</option> - <option value="55">55</option> - <option value="60">60</option> - <option value="62" selected="true">62</option> - <option value="65">65</option> - <option value="70">70</option> - <option value="75">75</option> - <option value="80">80</option> - <option value="85">85</option> - <option value="90">90</option> - <option value="95">95</option> - </param> - </when> - <when value="CODON"> - <param name="matrice" type="hidden" label="matrice" value="BLOSUM"/> - <param name="estimated" type="select" label="Estimated matrice BLOSUM"> - <option value="30">30</option> - <option value="35">35</option> - <option value="40">40</option> - <option value="45">45</option> - <option value="50">50</option> - <option value="55">55</option> - <option value="60">60</option> - <option value="62" selected="true">62</option> - <option value="65">65</option> - <option value="70">70</option> - <option value="75">75</option> - <option value="80">80</option> - <option value="85">85</option> - <option value="90">90</option> - <option value="95">95</option> - </param> - </when> - </conditional> - <param name="windowsSize" type="integer" label="Sliding Windows Size" min="1" value="3" - help="sliding window size (must be odd; ranges from 1 to alignment length; if - set to 1, then entropy-like values are not smoothed; default: 3)"/> - <param name="entropy_threshold" type="float" label="Maximum entropy threshold" value="0.5" min="0" max="1"/> - <param name="rateCutOff" type="float" label="Gap Rate cut-off [ 0-1 ]" value="0.5" min="0" max="1"/> - <param name="minBlock" type="integer" label="Minimum Block Size" value="5"/> - <param name="outputFormat" type="select" multiple="true" display="checkbox" label="Output file(s)"> - <option value="op" selected="true">Phylip</option> - <option value="of">Fasta</option> - <option value="on">Nexus</option> - <option value="oh">HTML</option> - </param> - </inputs> - <outputs> - <data name="outputop" format="phylip" label="BMGE Cleaned sequences Phylip" from_work_dir="fileop"> - <filter>'op' in outputFormat</filter> - </data> - <data name="outputof" format="Fasta" label="BMGE Cleaned sequences Fasta" from_work_dir="fileof"> - <filter>'of' in outputFormat</filter> - </data> - <data name="outputon" format="Nexus" label="BMGE Cleaned sequences Nexus" from_work_dir="fileon"> - <filter>'on' in outputFormat</filter> - </data> - <data name="outputoh" format="html" label="BMGE Cleaned sequences Html" from_work_dir="fileoh"> - <filter>'oh' in outputFormat</filter> - </data> - </outputs> - <help> - -.. class:: infomark - -**BMGE version 1.12 , 2015** - - ------ - -============== -Please cite: -============== - -"BMGE_ (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments" - - -.. _BMGE: http://www.biomedcentral.com/1471-2148/10/210 - -**Alexis Criscuolo and Simonetta Gribaldo** - -BMC Evolutionary Biology 2010 - ------ - -=========== -Overview: -=========== - -BMGE (Block Mapping and Gathering with Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference. BMGE selects characters that are biologically relevant, thanks to the use of standard similarity matrices such as PAM or BLOSUM. Moreover, BMGE provides other character- or sequenceremoval operations, such stationary-based character trimming (that provides a subset of compositionally homogeneous characters) or removal of sequences containing a too large proportion of gaps. Finally, BMGE can simply be used to perform standard conversion operations among DNA-, codon-, RY- and amino acid-coding sequences. - - - </help> - <citations> - <citation type="doi">10.1186/1471-2148-10-210</citation> - </citations> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bmge/bmge.xml Mon Feb 06 09:06:14 2017 -0500 @@ -0,0 +1,138 @@ +<tool id="bmge" name="BMGE" version="1.12"> + <description>cleaning aligned sequences</description> + <edam_operations> + <edam_operation>operation_2089</edam_operation> + </edam_operations> + <requirements> + <requirement type="package" version="1.12">BMGE</requirement> + </requirements> + <command>BMGE -i $input + -t $dataType.codeSeq + -m $dataType.matrix$dataType.estimated + -w $windowsSize + -g $rateCutOff + -h $entropy_threshold + -b $minBlock + #for $output in $outputFormat.value + #if $output + -$output file$output + #end if + #end for + </command> + + <inputs> + <param name="input" format="fasta" type="data" label="Source file" help="Fasta format"/> + <conditional name="dataType"> + <param name="codeSeq" type="select" label="Sequence Coding"> + <option value="DNA">DNA</option> + <option value="AA">AA</option> + <option value="CODON">Codon</option> + </param> + <when value="DNA"> + <param name="matrix" type="hidden" label="matrix" value="DNAPAM"/> + <param name="estimated" type="integer" label="Name of the PAM matrix [ 1-500 ]" value="250" min="1" max="500"/> + </when> + <when value="AA"> + <param name="matrix" type="hidden" label="matrix" value="BLOSUM"/> + <param name="estimated" type="select" label="Estimated matrix BLOSUM"> + <option value="30">30</option> + <option value="35">35</option> + <option value="40">40</option> + <option value="45">45</option> + <option value="50">50</option> + <option value="55">55</option> + <option value="60">60</option> + <option value="62" selected="true">62</option> + <option value="65">65</option> + <option value="70">70</option> + <option value="75">75</option> + <option value="80">80</option> + <option value="85">85</option> + <option value="90">90</option> + <option value="95">95</option> + </param> + </when> + <when value="CODON"> + <param name="matrix" type="hidden" label="matrix" value="BLOSUM"/> + <param name="estimated" type="select" label="Estimated matrix BLOSUM"> + <option value="30">30</option> + <option value="35">35</option> + <option value="40">40</option> + <option value="45">45</option> + <option value="50">50</option> + <option value="55">55</option> + <option value="60">60</option> + <option value="62" selected="true">62</option> + <option value="65">65</option> + <option value="70">70</option> + <option value="75">75</option> + <option value="80">80</option> + <option value="85">85</option> + <option value="90">90</option> + <option value="95">95</option> + </param> + </when> + </conditional> + <param name="windowsSize" type="integer" label="Sliding Windows Size" min="1" value="3" + help="sliding window size (must be odd; ranges from 1 to alignment length; if + set to 1, then entropy-like values are not smoothed; default: 3)"/> + <param name="entropy_threshold" type="float" label="Maximum entropy threshold" value="0.5" min="0" max="1"/> + <param name="rateCutOff" type="float" label="Gap Rate cut-off [ 0-1 ]" value="0.5" min="0" max="1"/> + <param name="minBlock" type="integer" label="Minimum Block Size" value="5"/> + <param name="outputFormat" type="select" multiple="true" label="Output file(s)"> + <option value="op" selected="true">Phylip</option> + <option value="of">Fasta</option> + <option value="on">Nexus</option> + <option value="oh">HTML</option> + </param> + </inputs> + <outputs> + <data name="outputop" format="phylip" label="BMGE Cleaned sequences Phylip" from_work_dir="fileop"> + <filter>'op' in outputFormat</filter> + </data> + <data name="outputof" format="fasta" label="BMGE Cleaned sequences Fasta" from_work_dir="fileof"> + <filter>'of' in outputFormat</filter> + </data> + <data name="outputon" format="nexus" label="BMGE Cleaned sequences Nexus" from_work_dir="fileon"> + <filter>'on' in outputFormat</filter> + </data> + <data name="outputoh" format="html" label="BMGE Cleaned sequences Html" from_work_dir="fileoh"> + <filter>'oh' in outputFormat</filter> + </data> + </outputs> + <help> + +.. class:: infomark + +**BMGE version 1.12 , 2015** + + +----- + +============== +Please cite: +============== + +"BMGE_ (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments" + + +.. _BMGE: http://www.biomedcentral.com/1471-2148/10/210 + +**Alexis Criscuolo and Simonetta Gribaldo** + +BMC Evolutionary Biology 2010 + +----- + +=========== +Overview: +=========== + +BMGE (Block Mapping and Gathering with Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference. BMGE selects characters that are biologically relevant, thanks to the use of standard similarity matrixs such as PAM or BLOSUM. Moreover, BMGE provides other character- or sequenceremoval operations, such stationary-based character trimming (that provides a subset of compositionally homogeneous characters) or removal of sequences containing a too large proportion of gaps. Finally, BMGE can simply be used to perform standard conversion operations among DNA-, codon-, RY- and amino acid-coding sequences. + + + </help> + <citations> + <citation type="doi">10.1186/1471-2148-10-210</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bmge/tool_dependencies.xml Mon Feb 06 09:06:14 2017 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="BMGE" version="1.12"> + <repository changeset_revision="f0e1947c756c" name="package_bmge_1_12" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>
--- a/tool_dependencies.xml Wed Dec 21 07:54:36 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="BMGE" version="1.12"> - <repository changeset_revision="dc960bad3690" name="package_bmge_1_12" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>