Galaxy |

Changeset 0:daf61c79c8b4 (2018-04-12)

Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks commit 2c1d4da58bb81f0b7232a1b3f0b3a0fde752de33

added:
gblocks.xml
test-data/Gblocks_Results_And_Parameters_on_data_95_html.html
test-data/Gblocks_Selected_Blocks_on_data_95.txt
test-data/Gblocks_on_data_95.txt
test-data/nad3.fasta

diff -r 000000000000 -r daf61c79c8b4 gblocks.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gblocks.xml Thu Apr 12 06:59:23 2018 -0400

[

@@ -0,0 +1,123 @@
+<tool id="gblocks" name="Gblocks" version="0.91b">
+ <description>Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis</description>
+ <requirements>
+ <requirement type="package" version="0.91b">gblocks</requirement>
+ </requirements>
+ <command><![CDATA[
+ln -s '$inputFile' input.pir && Gblocks
+input.pir
+-t=$t
+#if $advanced.a == '-a'
+ #if str($advanced.b1)
+ -b1=$advanced.b1
+ #end if
+ #if str($advanced.b2)
+ -b2=$advanced.b2
+ #end if
+ -b3=$advanced.b3
+ -b4=$advanced.b4
+ -b5=$advanced.b5
+ -b6=$advanced.b6
+ -b0=$advanced.b0
+#end if
+#set $output_opt = ''
+#if $outputs
+ #set $outputs_arr = str($outputs).split(',')
+ #for $o in $outputs_arr
+ #set $output_opt += $o + '=y '
+ #end for
+#else
+ #set $outputs_arr = []
+#end if
+#if $output_opt
+ #set $output_opt = $output_opt[:-1]
+#end if
+$output_opt
+> '$outputFile'
+ ]]></command>
+ <inputs>
+ <param name="inputFile" type="data" format="fasta,pir" label="Multiple Sequence Alignment" help="Multiple Sequence Alignment in Fasta format." />
+ <param argument="-t" type="select" label="Type Of Sequence">
+ <option value="p" selected="true">Protein</option>
+ <option value="d">DNA</option>
+ <option value="c">Codons</option>
+ </param>
+ <conditional name="advanced">
+ <param name="a" type="select" label="Specify Advanced Parameters">
+ <option value="-a">Yes</option>
+ <option value="" selected="true">No</option>
+ </param>
+ <when value="" />
+ <when value="-a">
+ <param argument="-b1" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a conserved position" help="Any integer bigger than half the number of sequences and smaller or equal than the total number of sequences" />
+ <param argument="-b2" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a flank position" help="Any integer equal or bigger than minimum number of sequences for a conserved position" />
+ <param argument="-b3" type="integer" value="8" label="Maximum number of contiguous nonconserved positions" />
+ <param argument="-b4" type="integer" value="10" min="2" label="Minimum length of a block" />
+ <param argument="-b5" type="select" label="Allowed gap positions">
+ <option value="n" selected="true">None</option>
+ <option value="h">With Half</option>
+ <option value="a">All</option>
+ </param>
+ <param argument="-b6" type="select" label="Use similarity matrices">
+ <option value="y" selected="true">Yes</option>
+ <option value="n">No</option>
+ </param>
+ <param argument="-b0" type="integer" value="10" min="2" label="Minimum length of an intial block" />
+ </when>
+ </conditional>
+ <param name="outputs" type="select" multiple="true" optional="true" display="checkboxes" label="Output formats">
+ <option value="-s" selected="true">Selected blocks</option>
+ <option value="-p" selected="true">Results and parameters File</option>
+ <option value="-n">Nonconserved blocks</option>
+ <option value="-u">Ungapped alignment</option>
+ <option value="-k">Mask file with the selected blocks</option>
+ <option value="-d">Postscript file with the selected blocks</option>
+ </param>
+ </inputs>
+ <outputs>
+ <data name="outputFile" format="txt" label="${tool.name} on ${on_string}" />
+ <data name="Results_and_parameters_file" format="html" from_work_dir="input.pir-gb.htm" label="${tool.name} Results and parameters on ${on_string}" >
+ <filter>outputs and '-p' in outputs</filter>
+ </data>
+ <data name="Selected_blocks" format="txt" from_work_dir="input.pir-gb" label="${tool.name} Selected blocks on ${on_string}" >
+ <filter>outputs and '-s' in outputs</filter>
+ </data>
+ <data name="Nonconserved_blocks" format="txt" from_work_dir="input.pir-gbComp" label="${tool.name} Nonconserved blocks on ${on_string}" >
+ <filter>outputs and '-n' in outputs</filter>
+ </data>
+ <data name="Ungapped_alignment" format="txt" from_work_dir="input.pir--" label="${tool.name} Ungapped alignment on ${on_string}" >
+ <filter>outputs and '-u' in outputs</filter>
+ </data>
+ <data name="Masked_file_with_the_selected_blocks" format="txt" from_work_dir="input.pir-gbMask" label="${tool.name} Masked file with the selected blocks on ${on_string}" >
+ <filter>outputs and '-k' in outputs</filter>
+ </data>
+ <data name="Postscript_file_with_the_selected_blocks" format="eps" from_work_dir="input.pir-gbPS" label="${tool.name} Postscript on ${on_string}" >
+ <filter>outputs and '-d' in outputs</filter>
+ </data>
+ </outputs>
+ <tests>
+ <test>
+ <param name="inputFile" ftype="fasta" value="nad3.fasta" />
+ <param name="-t" value="p" />
+ <param name="outputs" value="-s,-p" />
+ <output name="outputFile" file="Gblocks_on_data_95.txt" />
+ <output name="Results_and_parameters_file" file="Gblocks_Results_And_Parameters_on_data_95_html.html" />
+ <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
+ </test>
+ <test>
+ <param name="inputFile" ftype="fasta" value="nad3.fasta" />
+ <param name="-t" value="p" />
+ <param name="outputs" value="-s" />
+ <output name="outputFile" file="Gblocks_on_data_95.txt" />
+ <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
+ </test>
+ </tests>
+ <help><![CDATA[
+Simple wrapper for `Gblocks`_. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
+
+.. _Gblocks: http://molevol.cmima.csic.es/castresana/Gblocks.html
+ ]]></help>
+ <citations>
+ <citation type="doi">10.1093/oxfordjournals.molbev.a026334</citation>
+ </citations>
+</tool>

diff -r 000000000000 -r daf61c79c8b4 test-data/Gblocks_Results_And_Parameters_on_data_95_html.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gblocks_Results_And_Parameters_on_data_95_html.html Thu Apr 12 06:59:23 2018 -0400

[

b'@@ -0,0 +1,124 @@\n+<html>\n+<head>\n+<meta http-equiv=content-type content=text/html;charset=ISO-8859-1>\n+<title>input.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: input.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: 10\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 input.pir-gb: 56 (36% of the original 153 positions)\n+\n+\n+</body>\n+</html>\n'

diff -r 000000000000 -r daf61c79c8b4 test-data/Gblocks_Selected_Blocks_on_data_95.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gblocks_Selected_Blocks_on_data_95.txt Thu Apr 12 06:59:23 2018 -0400

@@ -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 000000000000 -r daf61c79c8b4 test-data/Gblocks_on_data_95.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Gblocks_on_data_95.txt Thu Apr 12 06:59:23 2018 -0400

@@ -0,0 +1,8 @@
+
+17 sequences and 153 positions in the first alignment file:
+input.pir
+
+input.pir
+Original alignment: 153 positions
+Gblocks alignment: 56 positions (36 %) in 3 selected block(s)
+

diff -r 000000000000 -r daf61c79c8b4 test-data/nad3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nad3.fasta Thu Apr 12 06:59:23 2018 -0400

@@ -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----------------------*