# HG changeset patch
# User dcorreia
# Date 1486389974 18000
# Node ID a943abb980db57d938e2474d9a4a6c79be1af2eb
# Parent c348ec5aebccf1da8adb633e4e14005d879de808
planemo upload commit e0ca504b3313992020acf8ab7aed0a261237766e-dirty
diff -r c348ec5aebcc -r a943abb980db BMGE.xml
--- 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 @@
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- cleaning aligned sequences
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- operation_2089
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- BMGE
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- 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
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- 'op' in outputFormat
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- 'of' in outputFormat
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- 'on' in outputFormat
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- 'oh' in outputFormat
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-.. class:: infomark
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-**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.
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- 10.1186/1471-2148-10-210
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diff -r c348ec5aebcc -r a943abb980db bmge/bmge.xml
--- /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 @@
+
+ cleaning aligned sequences
+
+ operation_2089
+
+
+ BMGE
+
+ 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
+
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+ 'op' in outputFormat
+
+
+ 'of' in outputFormat
+
+
+ 'on' in outputFormat
+
+
+ 'oh' in outputFormat
+
+
+
+
+.. 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.
+
+
+
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+ 10.1186/1471-2148-10-210
+
+
diff -r c348ec5aebcc -r a943abb980db bmge/tool_dependencies.xml
--- /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 @@
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diff -r c348ec5aebcc -r a943abb980db tool_dependencies.xml
--- 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 @@
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