Mercurial > repos > fubar > weblogo3
changeset 0:cec2527697f6
Migrated tool version 0.1 from old tool shed archive to new tool shed repository
author | fubar |
---|---|
date | Tue, 07 Jun 2011 17:43:58 -0400 |
parents | |
children | a76ecde597e1 |
files | rgweblogo/README rgweblogo/rgClustal_testout.fasta rgweblogo/rgWebLogo3.xml rgweblogo/rgWebLogo3_test.jpg |
diffstat | 4 files changed, 168 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgweblogo/README Tue Jun 07 17:43:58 2011 -0400 @@ -0,0 +1,30 @@ +This is a Galaxy tool wrapper for weblogo3 already available as a web app at the site below but neat as a Galaxy tool + +It generates sequence logos from fasta files such as the alignments generated by clustalw + +Note that the image for the help must be in static/images for it to show up on the tool form - it's the same image as goes in test-data + +**Installation** + +Make sure weblogo3 is installed in your system python and is available on the path for all your nodes + +Move the test data files to your galaxy root test-data +Move the xml file to a subdirectory of your tools folder (eg rgenetics/) and then add a line in your tool_conf.xml to point there. +Run +sh run_functional_tests.sh -id weblogo3 +to make sure the tests work + +then restart Galaxy and you should be good to go. + + +**Attribution** + +Source for the weblogo3 python executable is at http://weblogo.berkeley.edu + +Written by Ross Lazarus for the Rgenetics project + +Copyright Ross Lazarus at gmail com 2011 + +All rights reserved. + +Released under the LGPL - see http://www.gnu.org/copyleft/lesser.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgweblogo/rgClustal_testout.fasta Tue Jun 07 17:43:58 2011 -0400 @@ -0,0 +1,48 @@ +>c_briggsae-chrII_+_ +---ATGAGCTTCCACAAAAGCATGAGCTTT +CTCAGCTTCTGCCACATCAGCATTCAAATG +ATC +>c_brenneri-Cbre_Contig60_+_ +---ATGAGCCTCCACAACAGCATGATTTTT +CTCGGCTTCCGCCACATCCGCATTCAAATG +ATC +>c_remanei-Crem_Contig172_-_ +---ATGAGCCTCTACAACCGCATGATTCTT +TTCAGCCTCTGCCACGTCCGCATTCAAATG +CTC +>c_elegans-II_+_ +---ATGAGCCTCTACTACAGCATGATTCTT +CTCAGCTTCTGCAACGTCAGCATTCAGATG +ATC +>c_briggsae-chrII_+_bar +---CCGGAGTCGATCCCTGAAT-------- +------------------------------ +--- +>c_brenneri-Cbre_Contig60fee_+_ +---ACGAAGTCGATCCCTGAAA-------- +-TCAGATGAGCGGTTGACCA---GAGAACA +ACC +>c_remanei-Crem_Contig172zot_-_ +---ACGAAGTCGGTCCCTATAAGGTATGAT +TTTATATGA----TGTACCATAAGGAAATA +GTC +>c_elegans-II_+_meh +---ACGAAGTCGGTCCCTGAAC--AATTAT +TT----TGA----TATA---GAAAGAAACG +GTA +>c_briggsae-chrIfooI_+_ +CGCACAAATATGATGCACAAATCCACAACC +TAAAGCATCTCCGATAACGTTGACCGAAGT +--- +>c_brenneri-Cbre_Contig60gak_+_ +CGCACAAATGTAGTGGACAAATCCGCATCC +CAAAGCGTCTCCGATAACATTTACCGAAGT +--- +>c_remanei-Crem_Contig172foo_-_ +AGCACAAATGTAATGAACGAATCCGCATCC +CAACGCATCGCCAATCACATTCACAGATGT +--- +>c_elegans-II_+_more +TGCACAAATGTGATGAACGAATCCACATCC +CAATGCATCACCGATCACATTGACAGATGT +---
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgweblogo/rgWebLogo3.xml Tue Jun 07 17:43:58 2011 -0400 @@ -0,0 +1,90 @@ +<tool id="weblogo3" name="Sequence Logo" version="0.1"> + <description>generator for fasta (eg Clustal alignments)</description> + <command> + weblogo -F $outformat -s $size -f $input -o $output -t "$logoname" + </command> + <inputs> + <page> + <param format="fasta" name="input" type="data" label="Fasta File" /> + <param name="logoname" label="Name for output logo - will appear on graphics" type="text" size="50" value="Galaxy/Rgenetics weblogo" /> + <param name="outformat" type="select" label="Output weblogo format" > + <option value="png" selected="True">PNG screen quality</option> + <option value="png_print">High quality printable PNG</option> + <option value="pdf">PDF</option> + <option value="jpeg">JPG</option> + <option value="eps">EPS</option> + <option value="txt">Text (shows the detailed calculations for each position - no image)</option> + </param> + <param name="size" type="select" label="Output weblogo size" > + <option value="large" selected="True">Large</option> + <option value="medium">Medium</option> + <option value="small">Small</option> + </param> + </page> + </inputs> + <outputs> + <data format="pdf" name="output" label="${logoname}_output.${outformat}"> + <change_format> + <when input="outformat" value="png_print" format="png" /> + <when input="outformat" value="png" format="png" /> + <when input="outformat" value="jpeg" format="jpg" /> + <when input="outformat" value="eps" format="eps" /> + <when input="outformat" value="txt" format="txt" /> + </change_format> + </data> + </outputs> + <tests> + <test> + + <param name="input" value="rgClustal_testout.fasta" /> + <param name = "logoname" value="Galaxy/Rgenetics weblogo" /> + <param name = "outformat" value="jpeg" /> + <param name = "size" value="medium" /> + + <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" /> + </test> + + </tests> + <help> + +**Note** + +This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history. + +A typical output looks like this + +.. image:: ./static/images/rgWebLogo3_test.jpg + +---- + +**Why use WebLogo in Galaxy?** + +Weblogo3_ is a good example of an easy to use tool and there are plenty of other web accessible weblogo generator sites available. + +However, none of those offer the combination of: + +1) persistence of analyses and data in multiple shareable histories, pages and libraries + +2) convenient access to shared data libraries, workflows and user controlled pages, and to 3rd party data sources like UCSC tables. + +3) analyses integrated with many other applicable generic and specialized tools already available for downstream processing. + +that you get for free when you use Galaxy. No muss; no fuss. + +---- + +**Attribution** + +Weblogo attribution and associated documentation are available at Weblogo3_ + +This wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts + +.. _Weblogo3: http://weblogo.berkeley.edu/ + +.. _LGPL: http://www.gnu.org/copyleft/lesser.html + + </help> + +</tool> + +