Mercurial > repos > peterjc > mira_assembler

changeset 9:5573d802e431 draft

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Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub.
author peterjc
date Wed, 18 Sep 2013 06:22:19 -0400
parents 4266cccbb45a
children a2fb1e67bd11
files test-data/tvc_contigs.fasta test-data/tvc_mini.fastq tools/mira_3_4/README.rst tools/mira_3_4/mira.txt tools/mira_3_4/mira.xml tools/mira_3_4/tool_dependencies.xml
diffstat 6 files changed, 251 insertions(+), 127 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tvc_contigs.fasta	Wed Sep 18 06:22:19 2013 -0400
@@ -0,0 +1,20 @@
+>mira_c1
+ttagcgtggtcgcggccgaggtaccctctaccatgaaaccaggcttgggtccctctggct
+gtctcttggtgctgataatcttaccttgtgccttggcctcagccttcaacttatcgttct
+tcttgatcctctccatgatctcctcatggcaccttgatggctggacatgttccacacgaa
+catgaatcctcttccttatgattctgtttccaacctgcttgttgacctcaacaccaacag
+cacgcttggtgacgttccatacccgacccgtgcggccatgatagaacttgtggggcatac
+ctttgtggatcgacccgttaaccttgacatcaacatagtcgccgactttgaagatacgaa
+ggtaagttgtgagatgggtaggacccttcttcctgaatgcccgagcaaatagatctctgg
+tgcgcgaccccaaaccgtgacccgccggcattttgcggtgtttttcagacctgcccgggc
+ggccgctcgaaa
+>mira_c2
+tttcgagcggycgcccggscgaggtaccctscaccatgaaaccaggcttgggtccctcwg
+gctgyctcttggtgctgataatcttwccytgtgccttkgcctcagccttcaacttatcrt
+tcttcttgatcctctccattatctcctcatggcamckagatggctggacatgttccacac
+gaacatgaatcctcttccttatgattctgtttccaacctgyttgttgacctcaacaccaa
+cagcgcgcttggtgacgttccatacccgacccgtgcggccatggtagaacttgtggggca
+tacctttgtggatcgacccgttaaccttgacatcaacatagtcgccgactttgaagatac
+gaaggtaagttgtgagatgggtaggacccttcttcctgaatgcccgagcaaatagatccc
+tggtgcgtgacctcaaaccgtgacccgccggcattttgaggtgtttttcagacctgcccg
+ggcggccgctcgaaa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tvc_mini.fastq	Wed Sep 18 06:22:19 2013 -0400
@@ -0,0 +1,24 @@
+@gnlti136477918
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTACCCTCCACCATGAAACCAGGCTTGGGTCCCTCAGGCTGCCTCTTGGTGCTGATAATCTTTCCCTGTGCCTTTGCCTCAGCCTTCAACTTATCATTCTTCTTGATCCTCTCCATTATCTCCTCATGGCAACGAGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATCCTGTTACCAACCTGTTTGTTGACCTCAACACCAACAGCGCGCTTGGTAACATTCCAGACCCGACCCGTGCGCCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGCCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGCCCGAGCAAATAGATCCCTGGTGCGTGAACTCAAACCGTGACCCGCCGGCATTTTGAGGTGTTTTTCAGCTGCCTTGTTCACXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
++
+38<>><><<96-++42:AABBCCCCCCCCDFFFIYYIIIIIINTTTTNNNNNNTTTTTTNNIIIIHHHHHHYIFFFIDIINIITTTOQDDDHHHNTYTFFFIIINNIITDDDDDDFLLTTTLLLYYYYYYFFIIIILKOOYYYNNNNNNOOKKKKILLLFFIOOTTNLLLLLNYYYYKYFDDDLLLNNNTTNNLMKKSYNNJIIGGGGLLIILOOYYYYYYYYYTNNNNNTYYYYYYYTOLLLLLLNTTYYTTTLLTYYKKKONNNNLLLLGGINIIIIIINNNNNNNNIHHHHHHHHHHINIITTTTNNNNNTYTNNNNIIIFFDHHHFFINNNNIHHHDDEIDDDNNDDKQQQQMMMQQYYNNIDCBBBBAHIGGGKYYYOOD?<AACCCCCHCCC@>>>>HBBAAAA>@999AOOOYIIICC<<,,,99HHHFKK??C>>B>>H?6/+))42856301:7<>HHEI4/))-10449--0..((*4))*35A<9+++44>BB754---@<;42*))45:7024.(')))')++049>>41-'(,'(.2393222/3171((((-.4011/0+).)''),..4133><B=451119411+))<44:686:/066888888=::884))*'''**,''*-.''*,/2(*144+')64>;1/,'')''1*30+0..****(*0-.4-)*),'(''+,-((*+))**+,''''''***''***-*)121,''''(+*,,+-((****.0..,0*))*(),))''))*+,*)()))''''+'')'')**)()'','')'(**((*((*(((*441.-*****())+*''')-++*****-*((((**))))))*)))++***)(**11.()****0*-,((*--.***,((,,,**'')'''')'-((--,''**441***)+'(''*,*(
+@gnlti136478624
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAGCGTGGTCGCGGCCGAGGTACCCTCTACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCACGCTTGGTGACGTTCCATACCCGACCCGTGCGGCCATGATAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGGCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGGCCGAGCAAATAGATCTCTGGGTGCGGGAACTCAAACCGGGAACCGGCGGCATTTTGCGGTGTTTTTAGACCCTGCCGGGGGGGCGGTCGAAAGGCCGATTCTTGAGATTTTCCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGGGGGTAGGAGGTTGTAATTGGAAAAACCTGGGGTAGCAAGTTAATGGCTTGAGCAATTCCGTTCGGCGGGTGGGTATAGAGAAGGGGCGGGCGATCGGGATCCGAAGATGGGGAGCGGATGGGGAGGAGAGGCAGGTGGGGATATAGGGGGGGGGTGGGGTAGGGGAGGGGCGGTGCTGTAGGGGGAGGGGCGGCGTTGGTTTTCTGTGTTACGAGTTGGGTGACCCGAAGTAATTGGGG
++
++1449>>>;=::AADDCCCCFIICCBB>???BBDDDDYYHBCCBBFF@@777BBG@>7584;;@DHDDDDDDMNIIIIIYYYTOYKKKMIDDDDDHOKKKQSTTTNNIIYYFFFFFIDDDDDIYOOIIDAA>DADDFDLLDDDIKKKKOKKKKKKYYYOOJJJOYYYYTOOKKPMMMMMSSSSMMMSSYYYYLJIIIID=====FKKKKKKYYYOOKKIIIIISSFFDIHIIKSSTOOKKKLYYSSKMIIIOOIIIDDDDHDDDIOOIIFFFIIIIKKKMIIIIIIMKKKKIIIFDDDDADDIDDDDDDDHDDDDFFF99///<<HFFFFFFFFGOOYTDDDHHH99,,,95>>>>47//-</3-822.446777BBBFFIOC>6.++-53:?:>7744213...772007:9:-++33>>DH>>??933;;FQ<93/+10++/.//-10234:1//223;:/,,***++'')'+,/)))-.2.++((.0***,))*,0(())''))))+'')***''))***))),669+,*****..''')*,**,*))))*'',)))'(++,++((*+*)*.*))''')***''.*))'')''''''***+)))++**(''''')****)''')'(***''**+/.)))*)')((''***(('')'')-))''''.'')))**'+''''**))''))***+((***)%(((***(((((,.,,(((((*(((+.(()'''')*(())(***((**-+,,)')''*/,''''**'''))((''*+((''''))*))'')'')),.)())'''''('*)**+***-*(')''))((+++0***(('')'')**()++*+**(')).5+*'''')*,---'''')'''
+@gnlti136478626
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCTCAAAATGCCGGCGGGTCACGGTTTGAGGTCACGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATCTCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGTCGATCCACAAAGGTATGCCCCACAAGTTCTACCATGGCCGCACGGGTCGGGTATGGAACGTCACCAAGCGCGCTGTTGGTGTTGAGGTCAAGCATGAGGTGGGAAACAGAATCATAAGGAAAAGGATTCATGTGCGTGTGGAAGATGGTCAGGGATCGAGGTGCCATGAGGAGATCATGGTGAGGATCGAGAAGAACGATTAAGGGGAAGGCTGAGGGCGAGGGACAAGGTAAGATTATCAGCGACAAGAGACAAGCGGAGGGAGCCACGGCTGGGTGTGTGGTAGAGGGTGCCTCGGGCCGGGGCAAGGCTAAGCCGAATGCTGGGGATATTCATTAGACTGGGGGGCGGTCGAGGGTGGGTCGTAATGGGCCATTTGCGCGTATGGTGGGGTTGTTTGACATTGCGCTGGCCTCGGTTTACAGGGTTGTGATTGGAAAGCCGTGCGGTTGCCAACGTTAGTGTTTGGGAGACGTTCGCGTTCGGGGGCTGGGGTATTAAGGGGGGTCTGGGGTAAGGGCGTGCGAGGATGGTGGAGGGGTTTGGGGTTGGGCGTCTGTTTCGGGGTTTGTGGCGGGGGGTTGGTGGTTGCGTGACGGTGGGGGGGTTGGGCAGGCTATGGCGGGGCGTGGTGTTGGTCTGGTTGTGAGGATGTGAGTGTGCGTTGTTGTGTATTGGGACAGGT
++
+))..28:>C>CDDDDDDCCCCDDD>>A990028>HFFFIIFDDDDDHOTYYNGFAAAA;>??BQQIDDDIDIIIIGMMDDDDDDNIIIGGFFFFIMYKKIKKDD>D>>>C>D>><<<>::..'')46>IIIQIYYYMFDDAADKKKKYYYYYYNNDDDDIIGGKK777MMFFFKDDFAADDDDFKKKKFFFKIDDDDDDKIIIIEMFF=@@@B@BB??>O???OOTTTTLLKKK???DDDD>AAAA>B994B122:=B44/--447<155>>IIFFIKKKGGGGIIN944499C>>>>>>9</--7/00?;33/5/''''))**,.,,,2/0/20004449,,,-,6,--2:G>D>D74-++.15;911**+/-''))****-,''))1.2-.*****-<>71+**()+19:46.--+-*1611+*((****'''''(-/411-1***.((+***('**-8211,-**'''')+,,4,))''))))'')),,(')))).5++))'')).1-+,,.-+(''(++,,,('''))*''''))')+).''))*)-('')+)*((++.+++-*))('))''))+-0./,,))''))'')''*'')))''****.+*''*))'')'')'')))**+++))'''))'''*''*((****'''')'(,(''''''')*''))''))++*(((*((-))'')-)**()******042))***((*))''))*,-.((*)'')%%%)+++****((***-+*)''''))))''''))''''''')))),))***+('))))+.,)()+**''+.-)))(')''))'(***,(((,,***((((**++'')'(*))'''(**'''******((****//--))0+)''))*****))'')%%'')('*)))-(*01**))'((
+@gnlti136479063
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAGCGTGGTCGCGGCCGAGGTACCCTCTACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCGCGCTTGGTGACGTTCCATACCCGACCCGTGCGCCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGGCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGGCCGAGCAAATAGATCCCTGGTGCGTGAGCTCAAAGCGTGGACCGGCGGCATTTTAGGGTGTTTTTCAGCTGGCTCGGTGGTTTGAATGTGACTTGGGCGGGGGGGGGGTCGAAAGGCGAATTTGGAGATTTTCATAAAATTGGGGCGGTTGAAGATTGATTTTAAGGGGCAATTTGGGCTATAGGGGTGGTTTTAAATTAATGGGGGTGGTTTAAAAGTGTGATGGGGAAACGTGGGTTACCAATTTATGGGTGTGTGGAGTTCCCTTTGTGAGGTGGTATAGGAAAGGGGGGGCGTGACCTGCCACGTGGGGGGGGAAGTGTATGGGGGCGGGTTGGGGGGTTGAGGGGGGTGTGGGTGTGGGGGTGGGTTTTGTTAGGCGAGGTGGTTTTTTTTTCTTTTTTTTTTTAGTGGAGGTGT
++
+04--46:<<B<<>@>HHEB<822<<IEHIHCCCCCCIIIITTIIIIIINNTTTTTYTIHHHHHHNNNIIDDDDFFNTKM>>?OQFFFMKOOTFDDDDHHIIIIOHFFFFFINTDDAAAADHHDDDOYNNHHFFDDDDDDFDC=AA=DIIIIFFNHHFFFFNNNNNNNNNNDD448DNTOOKKKOBB?DFGGGNOTOO555>>A>>>AAF:::>>@DB=====5AACOIIBCCBB<5005<41''+18EAAAHHHB>96-+,+14:AAIB??>>CD>>;87>5:30-14477<>@CDDD>>?==MQYI>H---88:77:<B>>=33000008<9::>BBBFHHCCC>IFDDDOOOQIQQII:2((+6<552228>DDDEH>>33399>31)''-.FFIMIIIO>>333;@II>71:37<AAEIAA778<B69,,,01BBIKFF>>>944,,,6:6/(((*44<<43,,,66AEH98,,,6/+**--..((*,1><::65/0*'))'(,-,)++*31+((*((**.,+*'')'()'''*++))''('*+26410''''+)(())''))*'(***++*))*((****(''''')++**)+'')*))*.-***))*)*-/****,-30.)''''''''***''''')-.*))'')''**++*))/,,((,+-***+)'''''')+'''.*)')'(0-+((+++)))'''(*+'''')'(**,***''''))*))'')))),''))''))*((***))/()(*''''++**((((((****(')))))*))'),))'')''.)))))))'')+,++')-))'(+))***))''))****++))))+1-**))**'(140''))**))'')+**(
+@gnlti136479357
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTGTGGTCGCGGCCGAGGTACCCTGCACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCGCGCTTGGTGACGTTCCATACCCGACCCGTGCGGCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGCCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGCCCGAGCAAATAGATCCCTGGTGCGTGGACTCCAAACGTGAACTTGCCGGGCGGGGGGGAGAGGGGGAGCGGGGGGGGGGGAGAATAAGGGGGGAGGGGAGGGGGAGAGAAAAGGGAGGAGGGGGGGGGTAGGGAGGGAGAGGGAGGGGGGAGGGGGGGGGAGGGGGGGGGGGGAGGGAAGGGGGGGGAGGGGGGGAGGGGGAGGGGAGAGGGGGAGGGGAGGGGGGGGGGAGGGGAGGGGAAGAGGGGGGGGGGGGGGGGGGGAGGGGGGGAGGGGGGGGGGGAGGGGGGGGGGGGGGAGGGAGAAGGAGAAA
++
+.4<BB;>>>>>>>>FDCCCCCCIINIIIDCCCCCCDDDDYQKKFNNNCAAAAAINNIIINTIIHHDDDDDDDDDDDKITTTTLYYYYYLFFIIIILOKKKIIIIKKOKYFDDDDDFIIIIIKKKLLLLTIDDDDDFFDDDDDNNIIIIIKKDDDDHHJOYYSSMMFFADDDDLYSSB>666>BDDDDKOOKJJOOJJED==99AOIJJOOYYYLJJJLLTTTTLYYYYYYYYYYLLIIBBADDNOIIIIIINDAADDDDKOOIIIIIFDDA>7==@@DII??887BBOOFDDDDDIYYNNNHDDKOO?BBHHINODDAF>A>AADFFIIOGFFFFIITOOIDDDDDDDDDDDHHD89,,,<>FFFDD>99<<<B<845;<BAAA;>99=EBIIIIIOOD@@><>AB<8::AA:>AABHIHHHCCC99--+46CCCIIIIAA551-4440++)))4499+))019<>>>1/()0/-('''129.,//+((**+++8@@,*)11))*+***+++))%(,.*)))..,.2+**+8..)))),*))'')))''.''+)*++)+)))''))'(++++*))'''''))****))''))/.03:=741.''**),''''**))))))4**)')'').11.('*))'%)*-.2))*.0('''))(')''))****))('+'')''))****,((((**))1..''))***)1-1-.''),,''))%(.**)(')))*)-().-.***))1)''+''))****))''
+@gnlti136479522
+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCGCAAAATGCCGGCGGGTCACGGTTTGGGGTCGCGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATCTCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGTCGATCCACAAAGGTATGCCCCACAAGTTCTATCATGGCCGCACGGGTCGGGTATGGAACGTCACCAAGCGTGCTGTTGGGTGTNGAGGTCAAAAGCAAGTTGGAAACAGAATCATAAGGAAGAGGATTCATGTCCGTGTGGAACATGTCCAGCCATCAAGGTGCCATGAGGAGATCATGGAGAGGATCAAGAAGAACGATTAAGTGAAGGCTGAGGGCAAGGCACAAGGTATGATTATCAGGACCAAGAGACAGGCAGAGGGGACCAAGGCCTGGTTTCATGGGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
++
+(/..2>>H@CACCHICCCCCCIIYTTTFA>>>ADIIIIOTNNNNNIKINIIHDDDIIIHOMMFNNHDDDDDFINIIKOKKKFFIIIITYTLYIIIIIINTTTIFFFFFKLLYYYYYNNNNHHDDDGGNYYYYYYFDGDDDTHIIIIIIIKFFFIIITYINIIIITTTTYYYYTTNNNNNNNIIIIIIIIIFFIOOOOOIFFFFIIINOFKKNND84**+::FFFDHDDDDDIDD>44***49IIIFCIA?94233AIIIMQOOBFF:4-***66CCCCD>>444>?B44*((***45C>@BHIAAAA94%!%44=1-''''))''+(+/,((*245411.40)((+4::79..***-+/.()14BEEIIBCFIIHD88,,,NBID>>A>BB?AAAA>H:::;::4-+,,4/;46,**4841))/1.''*)))+444+++520'')11)(*.+,0**0((*159501224594406652//-/-2,/*1*')+.()./1.01::>>>>5511.4***1:5*((,-/-((******+*-'')((/20-)-,-*++.1/.(())''),351''))'(..280.'')+()**,398..''))**((+1.(())''))**-.--,,**''*)((-)***(()),1,/.1,))))+,+*+*++,-,'''')**((+*++,))))''))**1.,,***+****,+**+++4***.*))'')'')))''))*.5811.--+,+*+*))+,,-..+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/README.rst	Wed Sep 18 06:22:19 2013 -0400
@@ -0,0 +1,123 @@
+Galaxy tool to wrap the MIRA sequence assembly program (v3.4)
+=============================================================
+
+This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below (MIT licence).
+
+This tool is a short Python script (to collect the MIRA output and move it
+to where Galaxy expects the files, and convert MIRA's TCS file into a tab
+separated file for use in Galaxy).
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and
+install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
+and run any tests.
+
+
+Manual Installation
+===================
+
+There are just two Galaxy files to install:
+
+* mira.py (the Python script)
+* mira.xml (the Galaxy tool definition)
+
+The suggested location is a new tools/mira_3_4 folder. You will also need to
+modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
+this to tools_conf.xml.sample in order to run any tests::
+
+  <tool file="mira_3_4/mira.xml" />
+
+You will also need to install MIRA, we used version 3.4.1.1. See:
+
+* http://chevreux.org/projects_mira.html
+* http://sourceforge.net/projects/mira-assembler/
+
+WARNING: This tool was developed to construct viral genome assembly and
+mapping pipelines, for which the run time and memory requirements are
+negligible. For larger tasks, be aware that MIRA can require vast amounts
+of RAM and run-times of over a week are possible. This tool wrapper makes
+no attempt to spot and reject such large jobs.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version (working prototype, using MIRA 3.2.1)
+v0.0.2  - Improve capture of stdout/stderr (should see it as it runs)
+v0.0.3  - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
+          (some other switches changed, e.g. -OUT rrol to rrot, which
+          means the wrapper no longer works with MIRA 3.2.x)
+        - The contig summary file (TCS file) was removed in MIRA 3.4
+        - Report all missing output files (not just first missing one)
+v0.0.4  - Fix problem with backbone arguments inroduced in v0.0.3
+v0.0.5  - Implement the <version_command> tag to record the wrapper
+          version and the MIRA version being used.
+        - Check using MIRA 3.4 (later versions have a different API)
+v0.0.6  - Tell MIRA to use /tmp for temporary files
+        - Tell MIRA to ignore long read names (otherwise it aborts)
+v0.0.7  - Automated installation of the 64 bit Linux MIRA binary.
+v0.0.8  - Basic unit test added (but commented out due to Galaxy issue).
+        - Link to Tool Shed added to help text and this documentation.
+        - Use reStructuredText for this README file.
+        - Adopted standard MIT licence.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf mira_wrapper.tar.gz tools/mira_3_4/README.rst tools/mira_3_4/mira.xml tools/mira_3_4/mira.py tools/mira_3_4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
+
+Check this worked::
+
+    $ tar -tzf mira_wrapper.tar.gz
+    tools/mira_3_4/README.rst
+    tools/mira_3_4/mira.xml
+    tools/mira_3_4/mira.py
+    tools/mira_3_4/tool_dependencies.xml
+    test-data/tvc_mini.fastq
+    test-data/tvc_contigs.fasta
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
--- a/tools/mira_3_4/mira.txt	Wed Apr 24 12:43:17 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-Galaxy tool to wrap the MIRA sequence assembly program (v3.4)
-=============================================================
-
-This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (to collect the MIRA output and move it
-to where Galaxy expects the files, and convert MIRA's TCS file into a tab
-separated file for use in Galaxy).
-
-
-Automated Installation
-======================
-
-This should be straightforward, Galaxy should automatically download and
-install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
-and run any tests.
-
-
-Manual Installation
-===================
-
-There are just two Galaxy files to install:
-
-* mira.py (the Python script)
-* mira.xml (the Galaxy tool definition)
-
-The suggested location is a new tools/mira_3_4 folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
-this to tools_conf.xml.sample in order to run any tests:
-
-<tool file="mira_3_4/mira.xml" />
-
-You will also need to install MIRA, we used version 3.4.1.1. See:
-
-http://chevreux.org/projects_mira.html
-http://sourceforge.net/projects/mira-assembler/
-
-WARNING: This tool was developed to construct viral genome assembly and
-mapping pipelines, for which the run time and memory requirements are
-negligible. For larger tasks, be aware that MIRA can require vast amounts
-of RAM and run-times of over a week are possible. This tool wrapper makes
-no attempt to spot and reject such large jobs.
-
-
-History
-=======
-
-v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
-v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
-v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
-         (some other switches changed, e.g. -OUT rrol to rrot, which
-         means the wrapper no longer works with MIRA 3.2.x)
-       - The contig summary file (TCS file) was removed in MIRA 3.4
-       - Report all missing output files (not just first missing one)
-v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
-v0.0.5 - Implement the <version_command> tag to record the wrapper
-         version and the MIRA version being used.
-       - Check using MIRA 3.4 (later versions have a different API)
-v0.0.6 - Tell MIRA to use /tmp for temporary files
-       - Tell MIRA to ignore long read names (otherwise it aborts)
-v0.0.7 - Automated installation of the 64 bit Linux MIRA binary.
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-tar -czf mira_wrapper.tar.gz tools/mira_3_4/mira.*
-
-Check this worked:
-
-$ tar -tzf mira_wrapper.tar.gz
-tools/mira_3_4/mira.py
-tools/mira_3_4/mira.txt
-tools/mira_3_4/mira.xml
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
--- a/tools/mira_3_4/mira.xml	Wed Apr 24 12:43:17 2013 -0400
+++ b/tools/mira_3_4/mira.xml	Wed Sep 18 06:22:19 2013 -0400
@@ -1,7 +1,12 @@
-<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
+<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
     <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
-	<version_command interpreter="python">mira.py -v</version_command>
-	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
+    <requirements>
+        <requirement type="python-module">Bio</requirement>
+        <requirement type="binary">mira</requirement>
+        <requirement type="package" version="3.4.1.1">MIRA</requirement>
+    </requirements>
+    <version_command interpreter="python">mira.py -v</version_command>
+    <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
 ##Give the wrapper script list of output filenames, then the mira command...
 mira --job=$job_method,$job_type,$job_quality
 
@@ -52,7 +57,7 @@
 -DI:trt=/tmp
 
     </command>
-	<inputs>
+    <inputs>
         <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
             <option value="denovo">De novo</option>
             <option value="mapping">Mapping</option>
@@ -124,32 +129,63 @@
               <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
            </when>
         </conditional>
-	</inputs>
-	<outputs>
-	    <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
-	    <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
-	    <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
-	    <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
-	    <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
-	    <data name="out_log" format="txt" label="MIRA log" />
-	</outputs>
-	<tests>
-	</tests>
-	<requirements>
-		<requirement type="python-module">Bio</requirement>
-		<requirement type="binary">mira</requirement>
-	</requirements>
-	<help>
+    </inputs>
+    <outputs>
+        <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
+        <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
+        <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
+        <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
+        <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
+        <data name="out_log" format="txt" label="MIRA log" />
+    </outputs>
+    <tests>
+            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
+                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
+<!--
+Commenting out test until Galaxy framework is fixed,
+https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
+        <test>
+            <param name="job_method" value="denovo" />
+            <param name="job_type" value="est" />
+            <param name="job_qual" value="accurate" />
+            <param name="condBackbone.use" value="false" />
+            <param name="condSanger.use" value="true" />
+            <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
+            <param name="condRoche.use" value="false" />
+            <param name="condIllumina.use" value="false" /> 
+            <param name="condIonTorrent.use" value="false" />
+            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
+	</test>
+-->
+    </tests>
+    <help>
 
 **What it does**
 
 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
 
+MIRA is an open source assembly tool capable of handling sequence data from
+a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
+Ion Torrent).
+
+It is particularly suited to small genomes such as bacteria.
+
 **Citation**
 
-If you use this tool in scientific work leading to a publication, please cite:
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
 
-Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
+Chevreux et al. (1999).
+Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
+Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
 
-	</help>
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+
+    </help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/tool_dependencies.xml	Wed Sep 18 06:22:19 2013 -0400
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="MIRA" version="3.4.1.1">
+        <install version="1.0">
+            <actions>
+                <!-- Sourceforge doesn't offer nice clean download URLs which is a shame -->      
+                <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmira-assembler%2Ffiles%2FMIRA%2Fstable%2F&amp;ts=1366819213&amp;use_mirror=kent</action>
+                <!-- Currently we only need the main binary itself, mira -->
+                <action type="move_file"><source>mira_3.4.1.1_prod_linux-gnu_x86_64_static/bin/mira</source><destination>$INSTALL_DIR/</destination></action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Downloads MIRA v3.4 from Sourceforge, requesting Bastien's precompiled binaries
+for 64bit Linux (x86_64). He also has binaries for 32bit Linux, which we could
+use if/when the Galaxy installation framework allow that kind of flexibility.
+
+http://chevreux.org/projects_mira.html
+http://sourceforge.net/projects/mira-assembler/
+        </readme>
+    </package>
+</tool_dependency>
+