commit/galaxy-central: fubar: Added subsequence and colour options to weblogo3 sequence logo generator; tweaks to clustalw tool help
1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f2d655fb02d7/ changeset: r5254:f2d655fb02d7 user: fubar date: 2011-03-23 16:20:23 summary: Added subsequence and colour options to weblogo3 sequence logo generator; tweaks to clustalw tool help affected #: 2 files (1.3 KB) --- a/tools/rgenetics/rgClustalw.xml Wed Mar 23 10:59:26 2011 -0400 +++ b/tools/rgenetics/rgClustalw.xml Wed Mar 23 11:20:23 2011 -0400 @@ -79,7 +79,7 @@ <param name = "mode" value="complete" /><param name = "out_order" value="ALIGNED" /><output name="output" file="rgClustal_testout.fasta" ftype="fasta" /> - <output name="output" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /> + <output name="outlog" file="rgClustal_testout.log" ftype="txt" lines_diff="5" /></test></tests><help> @@ -109,9 +109,9 @@ The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz - see Clustfirst_ -It was modified by Ross Lazarus for the rgenetics project +It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added -This wrapper is now LGPL +This wrapper is released licensed under the LGPL_ .. _ClustalW2: http://www.ebi.ac.uk/2can/tutorials/protein/clustalw.html @@ -119,6 +119,8 @@ .. _Clustfirst: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003732.html +.. _LGPL: http://www.gnu.org/copyleft/lesser.html + </help></tool> --- a/tools/rgenetics/rgWebLogo3.xml Wed Mar 23 10:59:26 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.xml Wed Mar 23 11:20:23 2011 -0400 @@ -1,13 +1,16 @@ <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" + weblogo -F $outformat -s $size -f $input -o $output -t "$logoname" -c "$colours" +#if $range.mode == 'part' +-l "$range.seqstart" -u "$range.seqend" +#end if </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" > + <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="Galaxy-Rgenetics Sequence Logo" /> + <param name="outformat" type="select" label="Output format for image (or text report)" ><option value="png" selected="True">PNG screen quality</option><option value="png_print">High quality printable PNG</option><option value="pdf">PDF</option> @@ -15,6 +18,32 @@ <option value="eps">EPS</option><option value="txt">Text (shows the detailed calculations for each position - no image)</option></param> + <param name="colours" type="select" label="Colour scheme for output Sequence Logo" + help="Note that some of these only make sense for protein sequences!"> + <option value="auto" selected="True">Default automatic colour selection</option> + <option value="base pairing">Base pairing</option> + <option value="charge">Charge colours</option> + <option value="chemistry">Chemistry colours</option> + <option value="classic">Classical colours</option> + <option value="hydrophobicity">Hydrophobicity</option> + <option value="monochrome">monochrome</option> + </param> + + <conditional name="range"> + <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use"> + <option value="complete" selected="true">complete sequence</option> + <option value="part">Only use a part of the sequence</option> + </param> + <when value="complete"> + </when> + <when value="part"> + <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" + label="Index (eg 1=first letter) of the start of the sequence range to include in the logo"> + </param> + <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" > + </param> + </when> + </conditional><param name="size" type="select" label="Output weblogo size" ><option value="large" selected="True">Large</option><option value="medium">Medium</option> @@ -39,8 +68,9 @@ <param name="input" value="rgClustal_testout.fasta" /><param name = "logoname" value="Galaxy/Rgenetics weblogo" /><param name = "outformat" value="jpeg" /> - <param name = "size" value="medium" /> - + <param name = "range" value="complete" /> + <param name = "size" value="medium" /> + <param name = "colours" value="auto" /><output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" /></test> @@ -51,33 +81,21 @@ This tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history. +It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed +it in to this tool. + 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 +This Galaxy 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/ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.
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