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Changeset 3:baeab8664657 (2017-02-06)

Previous changeset 2:814b453382cf (2017-01-23)

Commit message:
planemo upload commit e0ca504b3313992020acf8ab7aed0a261237766e-dirty

added:
gblocks/gblocks.xml
gblocks/test-data/nad3.pir
gblocks/test-data/nad3.pir-gb
gblocks/test-data/nad3.pir-gb.htm
gblocks/tool_dependencies.xml

removed:
gblocks.xml
test-data/nad3.pir
test-data/nad3.pir-gb
test-data/nad3.pir-gb.htm
tool_dependencies.xml

diff -r 814b453382cf -r baeab8664657 gblocks.xml
--- a/gblocks.xml Mon Jan 23 07:42:56 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,112 +0,0 @@
-<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>

diff -r 814b453382cf -r baeab8664657 gblocks/gblocks.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gblocks/gblocks.xml Mon Feb 06 09:06:35 2017 -0500

@@ -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>

diff -r 814b453382cf -r baeab8664657 gblocks/test-data/nad3.pir
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gblocks/test-data/nad3.pir Mon Feb 06 09:06:35 2017 -0500

@@ -0,0 +1,101 @@
+>P1;nad3_parde
+
+------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF
+D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA
+YEWKKGALEWA----------------------*
+
+>P1;nad3_acaca
+
+---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF
+E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI
+YEWQKGALEWD----------------------*
+
+>P1;nad3_allma
+
+--------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL
+G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI
+YEFVSGAITDSF---------------------*
+
+>P1;nad3_apec
+
+-----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL
+N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI
+FEWVQGGLDWAE---------------------*
+
+>P1;nad3_arath
+
+---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS
+G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL
+YEWKRGASDRE----------------------*
+
+>P1;nad3_balca
+
+-------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ
+A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI
+YEWMEGGLEWAE---------------------*
+
+>P1;nad3_chocr
+
+------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF
+D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI
+YEWYKGALEWE----------------------*
+
+>P1;nad3_drome
+
+-------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK
+S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY
+HEWNQGMLNWSN---------------------*
+
+>P1;nad3_human
+
+-------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM
+S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA
+YEWLQKGLDWTE---------------------*
+
+>P1;nad3_ktun
+
+-------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK
+S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL
+HEWSEGSLEWFSSSN------------------*
+
+>P1;nad3_lter
+
+-------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK
+S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI
+HEWKEGSLDWSS---------------------*
+
+>P1;nad3_marpo
+
+-----------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF
+D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV
+YEWKKGALDWE----------------------*
+
+>P1;nad3_metse
+
+---------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF
+G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV
+YEWLKGGLEWE----------------------*
+
+>P1;nad3_picca
+
+MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF
+R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI
+IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--*
+
+>P1;nad3_podan
+
+-------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF
+LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV
+YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI*
+
+>P1;nad3_prowi
+
+----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF
+D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI
+YEWRKGALDWS----------------------*
+
+>P1;nad3_recam
+
+-----MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF
+D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI
+YEWKKGALDWE----------------------*

diff -r 814b453382cf -r baeab8664657 gblocks/test-data/nad3.pir-gb
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gblocks/test-data/nad3.pir-gb Mon Feb 06 09:06:35 2017 -0500

@@ -0,0 +1,68 @@
+>P1;nad3_parde
+
+EKVSAYECGF NAFARMKFDV RFYLVSILFI IFDLEVAFLF PVLTVGFAYE WKKGAL*
+
+>P1;nad3_acaca
+
+EKNSAYECGF QPFTRSKFNV RYYLIAILFM IFDLEIMYLF PILTVGFIYE WQKGAL*
+
+>P1;nad3_allma
+
+EKVSAYECGF SPLARQKFDV SFYLIAILFI IFDLEVVFIL PILTIGFIYE FVSGAI*
+
+>P1;nad3_apec
+
+EKSSPYECGF DPLARVPFSF RFFLVAILFL LFDLEIALLF PILTVGLIFE WVQGGL*
+
+>P1;nad3_arath
+
+EKLSAYECGF DPSARSRFDI RFYLVSILFL IPDLEVTFFF PILTIGFLYE WKRGAS*
+
+>P1;nad3_balca
+
+EKLSPYECGF DPQARLPFSL RFFLVAILFL LFDLEIALLL PILTIGLIYE WMEGGL*
+
+>P1;nad3_chocr
+
+EKVSAYECGF NPFARATFDI RFYLVAILFL IFDLEISFLF PILTIGFIYE WYKGAL*
+
+>P1;nad3_drome
+
+EKSSPFECGF DPKSRLPFSL RFFLITIIFL IFDVEIALIL PILLIGLYHE WNQGML*
+
+>P1;nad3_human
+
+EKSTPYECGF DPMARVPFSM KFFLVAITFL LFDLEIALLL PILALSLAYE WLQKGL*
+
+>P1;nad3_ktun
+
+EKSSPFECGF DPKARLPFSM RFFLITVVFL VFDVEIVLLL PILIIGVLHE WSEGSL*
+
+>P1;nad3_lter
+
+EKSSPFECGF DPKARIPFST RFFLLAIIFI VFDIEIVLLM PILLIGLIHE WKEGSL*
+
+>P1;nad3_marpo
+
+EKLSAYECGF DPFARSRFDI RFYLVSILFI IFDLEVTFLF PILTIGFVYE WKKGAL*
+
+>P1;nad3_metse
+
+EKVSAYECGF DPFPGRPFSI RFFLIGILFL IFDLEISFLF PVLTLGLVYE WLKGGL*
+
+>P1;nad3_picca
+
+NKTGPYECGF DSFSRTTYSI KFILIAILFL PFDLELTSIL PPLIIGFIIE INTKAI*
+
+>P1;nad3_podan
+
+EKYSIFECGF HSFNRTQFGV KFFIFALVYL LLDLEILLTF PIITIGFVYE LGKSAL*
+
+>P1;nad3_prowi
+
+EKISAYECGF DPFARGRFDI QFYLVAILFI IFDLEVAFLF PILTVGFIYE WRKGAL*
+
+>P1;nad3_recam
+
+EKLSPYECGF NPFARGAFDV RFYLVAILFI IFDLEVAFLF PILTVGFIYE WKKGAL*
+

diff -r 814b453382cf -r baeab8664657 gblocks/test-data/nad3.pir-gb.htm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gblocks/test-data/nad3.pir-gb.htm Mon Feb 06 09:06:35 2017 -0500

[

b'@@ -0,0 +1,124 @@\n+<html>\n+<head>\n+<meta http-equiv=content-type content=text/html;charset=ISO-8859-1>\n+<title>nad3.pir</title>\n+<style media=screen type=text/css></style>\n+</head>\n+\n+<body bgcolor=#f5f5a3>\n+<h2>Gblocks 0.91b Results</h2>\n+\n+Processed file: nad3.pir \n+Number of sequences: 17 Alignment assumed to be: Protein \n+New number of positions: 56 (selected positions are underlined in blue)\n+\n+<pre>\n+ 10 20 30 40 50 60\n+ =========+=========+=========+=========+=========+=========+\n+nad3_parde ------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF\n+nad3_acaca ---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF\n+nad3_allma --------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL\n+nad3_apec -----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL\n+nad3_arath ---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS\n+nad3_balca -------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ\n+nad3_chocr ------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECG#######\n+\n+\n+ 130 140 150\n+ =========+=========+=========+===\n+nad3_parde YEWKKGALEWA----------------------\n+nad3_acaca YEWQKGALEWD----------------------\n+nad3_allma YEFVSGAITDSF---------------------\n+nad3_apec FEWVQGGLDWAE---------------------\n+nad3_arath YEWKRGASDRE----------------------\n+nad3_balca YEWMEGGLEWAE---------------------\n+nad3_chocr YEWYKGALEWE----------------------\n+nad3_drome HEWNQGMLNWSN---------------------\n+nad3_human YEWLQKGLDWTE---------------------\n+nad3_ktun HEWSEGSLEWFSSSN------------------\n+nad3_lter HEWKEGSLDWSS---------------------\n+nad3_marpo YEWKKGALDWE----------------------\n+nad3_metse YEWLKGGLEWE----------------------\n+nad3_picca IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--\n+nad3_podan YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI\n+nad3_prowi YEWRKGALDWS----------------------\n+nad3_recam YEWKKGALDWE----------------------\n+ ######## \n+\n+\n+\n+</pre>\n+<pre>\n+\n+\n+ Parameters used\n+Minimum Number Of Sequences For A Conserved Position: 9\n+Minimum Number Of Sequences For A Flanking Position: 14\n+Maximum Number Of Contiguous Nonconserved Positions: 8\n+Minimum Length Of A Block: 5\n+Allowed Gap Positions: None\n+Use Similarity Matrices: Yes\n+\n+</pre><pre>Flank positions of the 3 selected block(s)\n+Flanks: [48 60] [64 91] [114 128] \n+\n+New number of positions in nad3.pir-gb1: 56 (36% of the original 153 positions)\n+\n+\n+</body>\n+</html>\n'

diff -r 814b453382cf -r baeab8664657 gblocks/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gblocks/tool_dependencies.xml Mon Feb 06 09:06:35 2017 -0500

@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+ <package name="gblocks" version="0.91b">
+ <repository changeset_revision="cc74017fbc04" name="package_gblocks_0_91b" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+ </package>
+</tool_dependency>

diff -r 814b453382cf -r baeab8664657 test-data/nad3.pir
--- a/test-data/nad3.pir Mon Jan 23 07:42:56 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,101 +0,0 @@
->P1;nad3_parde
-
-------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF
-D-DARMKFDVRFYLVSILFIIFDLEVAFLFPWAVSFASLS-DVAFWGLMVFLAVLTVGFA
-YEWKKGALEWA----------------------*
-
->P1;nad3_acaca
-
----------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF
-E-DTRSKFNVRYYLIAILFMIFDLEIMYLFPWSISISTGS-FFGVWAIFLFLIILTVGFI
-YEWQKGALEWD----------------------*
-
->P1;nad3_allma
-
---------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL
-G-DARQKFDVSFYLIAILFIIFDLEVVFILPFASVIHNVS-LLGGWITIIFLVILTIGFI
-YEFVSGAITDSF---------------------*
-
->P1;nad3_apec
-
------------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL
-N-SARVPFSFRFFLVAILFLLFDLEIALLFPLPFSVFFH--P--IHTP----LILTVGLI
-FEWVQGGLDWAE---------------------*
-
->P1;nad3_arath
-
----------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS
-G-DARSRFDIRFYLVSILFLIPDLEVTFFFPWAVPPNKID-LFGFWSMMAFLFILTIGFL
-YEWKRGASDRE----------------------*
-
->P1;nad3_balca
-
--------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ
-A-SARLPFSLRFFLVAILFLLFDLEIALLLPFPAALSARDPQLSFTLAFLILLILTIGLI
-YEWMEGGLEWAE---------------------*
-
->P1;nad3_chocr
-
-------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECGFNPF
-D-DARATFDIRFYLVAILFLIFDLEISFLFPWSLVLGEIS-IIGFWSMIVFLVILTIGFI
-YEWYKGALEWE----------------------*
-
->P1;nad3_drome
-
--------------MFSIIFIALLILLITTIVMFLASILSKKA-LIDREKSSPFECGFDPK
-S-SSRLPFSLRFFLITIIFLIFDVEIALILPMIIIMKYSNIMIWTITSIIFILILLIGLY
-HEWNQGMLNWSN---------------------*
-
->P1;nad3_human
-
--------------MN-FALILMINTLLALLLMIITFWLPQLN-GY-MEKSTPYECGFDPM
-S-PARVPFSMKFFLVAITFLLFDLEIALLLPLPWALQTTNLPLMVMSSLLLIIILALSLA
-YEWLQKGLDWTE---------------------*
-
->P1;nad3_ktun
-
--------------MFFVLSLVLFTFLLSLVLLSVSLSLTKKK-MMNREKSSPFECGFDPK
-S-SARLPFSMRFFLITVVFLVFDVEIVLLLPYLFSSGWSIDVFSLVGSMMILVILIIGVL
-HEWSEGSLEWFSSSN------------------*
-
->P1;nad3_lter
-
--------------MILTALSSAIALLVPIIILGAAWVLASRS-TEDREKSSPFECGFDPK
-S-TARIPFSTRFFLLAIIFIVFDIEIVLLMPLPTILHTSDVFTTVTTSVLFLMILLIGLI
-HEWKEGSLDWSS---------------------*
-
->P1;nad3_marpo
-
------------MEFAPIFVYLVISLLLSLILIGVSFLFASSSSLAYPEKLSAYECGFDPF
-D-DARSRFDIRFYLVSILFIIFDLEVTFLFPWAVSLNKIG-LFGFWSMMVFLFILTIGFV
-YEWKKGALDWE----------------------*
-
->P1;nad3_metse
-
----------MYTEFYGILVLLIFSVVLSAIISGASYILGDKQ--PDREKVSAYECGFDPF
-G-TPGRPFSIRFFLIGILFLIFDLEISFLFPWCVVCNQVF-PFGYWTMIVFLAVLTLGLV
-YEWLKGGLEWE----------------------*
-
->P1;nad3_picca
-
-MLNYFVYPYGIENDMGMKFYMMLVPMMSMVLMMINYMMTNKS-DNNMNKTGPYECGFDSF
-R-QSRTTYSIKFILIAILFLPFDLELTSILPYTLSMYNTN-IYGLFILLYFLLPLIIGFI
-IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--*
-
->P1;nad3_podan
-
--------------MSSMTLFILFVSIIALLFLFINLIFAPHN--PYQEKYSIFECGFHSF
-LGQNRTQFGVKFFIFALVYLLLDLEILLTFPFAVSEYVNN-IYGLIILLGFITIITIGFV
-YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI*
-
->P1;nad3_prowi
-
-----------MYEFLGILIYFFIALALSLLLLGLPFLVSTRK--ADPEKISAYECGFDPF
-D-DARGRFDIQFYLVAILFIIFDLEVAFLFPWALTLNKIG-YFGFWSMMLFLFILTVGFI
-YEWRKGALDWS----------------------*
-
->P1;nad3_recam
-
------MNTMILSEYLSVLIFFIFSFGLSCIILGLSYVLATQN--ADTEKLSPYECGFNPF
-D-DARGAFDVRFYLVAILFIIFDLEVAFLFPWAVALSDVT-IFGFWTMFIFLLILTVGFI
-YEWKKGALDWE----------------------*

diff -r 814b453382cf -r baeab8664657 test-data/nad3.pir-gb
--- a/test-data/nad3.pir-gb Mon Jan 23 07:42:56 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,68 +0,0 @@
->P1;nad3_parde
-
-EKVSAYECGF NAFARMKFDV RFYLVSILFI IFDLEVAFLF PVLTVGFAYE WKKGAL*
-
->P1;nad3_acaca
-
-EKNSAYECGF QPFTRSKFNV RYYLIAILFM IFDLEIMYLF PILTVGFIYE WQKGAL*
-
->P1;nad3_allma
-
-EKVSAYECGF SPLARQKFDV SFYLIAILFI IFDLEVVFIL PILTIGFIYE FVSGAI*
-
->P1;nad3_apec
-
-EKSSPYECGF DPLARVPFSF RFFLVAILFL LFDLEIALLF PILTVGLIFE WVQGGL*
-
->P1;nad3_arath
-
-EKLSAYECGF DPSARSRFDI RFYLVSILFL IPDLEVTFFF PILTIGFLYE WKRGAS*
-
->P1;nad3_balca
-
-EKLSPYECGF DPQARLPFSL RFFLVAILFL LFDLEIALLL PILTIGLIYE WMEGGL*
-
->P1;nad3_chocr
-
-EKVSAYECGF NPFARATFDI RFYLVAILFL IFDLEISFLF PILTIGFIYE WYKGAL*
-
->P1;nad3_drome
-
-EKSSPFECGF DPKSRLPFSL RFFLITIIFL IFDVEIALIL PILLIGLYHE WNQGML*
-
->P1;nad3_human
-
-EKSTPYECGF DPMARVPFSM KFFLVAITFL LFDLEIALLL PILALSLAYE WLQKGL*
-
->P1;nad3_ktun
-
-EKSSPFECGF DPKARLPFSM RFFLITVVFL VFDVEIVLLL PILIIGVLHE WSEGSL*
-
->P1;nad3_lter
-
-EKSSPFECGF DPKARIPFST RFFLLAIIFI VFDIEIVLLM PILLIGLIHE WKEGSL*
-
->P1;nad3_marpo
-
-EKLSAYECGF DPFARSRFDI RFYLVSILFI IFDLEVTFLF PILTIGFVYE WKKGAL*
-
->P1;nad3_metse
-
-EKVSAYECGF DPFPGRPFSI RFFLIGILFL IFDLEISFLF PVLTLGLVYE WLKGGL*
-
->P1;nad3_picca
-
-NKTGPYECGF DSFSRTTYSI KFILIAILFL PFDLELTSIL PPLIIGFIIE INTKAI*
-
->P1;nad3_podan
-
-EKYSIFECGF HSFNRTQFGV KFFIFALVYL LLDLEILLTF PIITIGFVYE LGKSAL*
-
->P1;nad3_prowi
-
-EKISAYECGF DPFARGRFDI QFYLVAILFI IFDLEVAFLF PILTVGFIYE WRKGAL*
-
->P1;nad3_recam
-
-EKLSPYECGF NPFARGAFDV RFYLVAILFI IFDLEVAFLF PILTVGFIYE WKKGAL*
-

diff -r 814b453382cf -r baeab8664657 test-data/nad3.pir-gb.htm
--- a/test-data/nad3.pir-gb.htm Mon Jan 23 07:42:56 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,124 +0,0 @@\n-<html>\n-<head>\n-<meta http-equiv=content-type content=text/html;charset=ISO-8859-1>\n-<title>nad3.pir</title>\n-<style media=screen type=text/css></style>\n-</head>\n-\n-<body bgcolor=#f5f5a3>\n-<h2>Gblocks 0.91b Results</h2>\n-\n-Processed file: nad3.pir \n-Number of sequences: 17 Alignment assumed to be: Protein \n-New number of positions: 56 (selected positions are underlined in blue)\n-\n-<pre>\n- 10 20 30 40 50 60\n- =========+=========+=========+=========+=========+=========+\n-nad3_parde ------MEYLLQEYLPILVFLGMASALAIVLILAAAVIAVRN--PDPEKVSAYECGFNAF\n-nad3_acaca ---------MTLEYIYIFIFFWGAFFISCLLIFLSYFLVYQE--SDIEKNSAYECGFQPF\n-nad3_allma --------------MTYLVYIVFTIVLTVGLILVSYLLSQAQ--PDSEKVSAYECGFSPL\n-nad3_apec -----------IFNFLTLFVSILIFLITTLITFAAHFLPSRN-TD-SEKSSPYECGFDPL\n-nad3_arath ---------MMSEFAPISIYLVISLLVSLILLGVPFPFASNS-STYPEKLSAYECGFDPS\n-nad3_balca -------------MNSFLIYLLIAITLSFILSIVGHRLPTRN-MD-QEKLSPYECGFDPQ\n-nad3_chocr ------MKLIFTEYSAILIFFAISSLLSSVIFLLSYFLIPQK--PDQEKVSAYECG#######\n-\n-\n- 130 140 150\n- =========+=========+=========+===\n-nad3_parde YEWKKGALEWA----------------------\n-nad3_acaca YEWQKGALEWD----------------------\n-nad3_allma YEFVSGAITDSF---------------------\n-nad3_apec FEWVQGGLDWAE---------------------\n-nad3_arath YEWKRGASDRE----------------------\n-nad3_balca YEWMEGGLEWAE---------------------\n-nad3_chocr YEWYKGALEWE----------------------\n-nad3_drome HEWNQGMLNWSN---------------------\n-nad3_human YEWLQKGLDWTE---------------------\n-nad3_ktun HEWSEGSLEWFSSSN------------------\n-nad3_lter HEWKEGSLDWSS---------------------\n-nad3_marpo YEWKKGALDWE----------------------\n-nad3_metse YEWLKGGLEWE----------------------\n-nad3_picca IEINTKAIYMTKMFNRNVKSMTSYVKYNNKI--\n-nad3_podan YELGKSALKIDSRQVITMTRFNYSSTIEYLGKI\n-nad3_prowi YEWRKGALDWS----------------------\n-nad3_recam YEWKKGALDWE----------------------\n- ######## \n-\n-\n-\n-</pre>\n-<pre>\n-\n-\n- Parameters used\n-Minimum Number Of Sequences For A Conserved Position: 9\n-Minimum Number Of Sequences For A Flanking Position: 14\n-Maximum Number Of Contiguous Nonconserved Positions: 8\n-Minimum Length Of A Block: 5\n-Allowed Gap Positions: None\n-Use Similarity Matrices: Yes\n-\n-</pre><pre>Flank positions of the 3 selected block(s)\n-Flanks: [48 60] [64 91] [114 128] \n-\n-New number of positions in nad3.pir-gb1: 56 (36% of the original 153 positions)\n-\n-\n-</body>\n-</html>\n'

diff -r 814b453382cf -r baeab8664657 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Jan 23 07:42:56 2017 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
- <package name="gblocks" version="0.91b">
- <repository changeset_revision="cc74017fbc04" name="package_gblocks_0_91b" owner="dcorreia" toolshed="https://testtoolshed.g2.bx.psu.edu" />
- </package>
-</tool_dependency>