3 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/63e0cc9ca457/ changeset: r5346:63e0cc9ca457 user: jgoecks date: 2011-04-05 20:12:39 summary: Trackster: mode is not reduced if in auto mode. affected #: 1 file (22 bytes) --- a/static/scripts/trackster.js Tue Apr 05 12:08:42 2011 -0400 +++ b/static/scripts/trackster.js Tue Apr 05 14:12:39 2011 -0400 @@ -2092,9 +2092,9 @@ update_auto_mode: function( mode ) { if ( this.mode == "Auto" ) { if ( mode == "no_detail" ) { - mode = "reduced to feature spans"; + mode = "feature spans"; } else if ( mode == "summary_tree" ) { - mode = "reduced to coverage histogram"; + mode = "coverage histogram"; } this.mode_div.text( "Auto (" + mode + ")" ); } http://bitbucket.org/galaxy/galaxy-central/changeset/6131f91bad52/ changeset: r5347:6131f91bad52 user: jgoecks date: 2011-04-05 20:14:32 summary: Merge. affected #: 3 files (740 bytes) --- a/tool_conf.xml.main Tue Apr 05 14:12:39 2011 -0400 +++ b/tool_conf.xml.main Tue Apr 05 14:14:32 2011 -0400 @@ -169,12 +169,6 @@ <!-- <tool file="hyphy/hyphy_dnds_wrapper.xml" /> --><tool file="evolution/mutate_snp_codon.xml" /></section> - <section name="Motif Tools" id="motifs"> - <tool file="rgenetics/rgWebLogo3.xml" /> - </section> - <section name="Multiple Alignments" id="clustal"> - <tool file="rgenetics/rgClustalw.xml" /> - </section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /> --- a/tools/rgenetics/rgCaCo.py Tue Apr 05 14:12:39 2011 -0400 +++ b/tools/rgenetics/rgCaCo.py Tue Apr 05 14:14:32 2011 -0400 @@ -53,28 +53,26 @@ resfl = resfl[1:] headl = [x.strip().upper() for x in headl] headIndex = dict(zip(headl,range(0,len(headl)))) - chrpos = headIndex.get('CHR',None) - rspos = headIndex.get('RS',None) - offspos = headIndex.get('OFFSET',None) - ppos = headIndex.get('LOG10ARMITAGEP',None) - wewant = [chrpos,rspos,offspos,ppos] + whatwewant = ['CHR','RS','OFFSET','LOG10ARMITAGEP'] + wewant = [headIndex.get(x,None) for x in whatwewant] if None in wewant: # missing something - logf.write('### Error missing a required header in makeGFF - headIndex=%s\n' % headIndex) + logf.write('### Error missing a required header from %s in makeGFF - headIndex=%s\n' % (whatwewant,headIndex)) return - resfl = [x for x in resfl if x[ppos] > ''] + ppos = wewant[3] # last in list + resfl = [x for x in resfl if x[ppos] > '' and x[ppos] <> 'NA'] resfl = [(float(x[ppos]),x) for x in resfl] # decorate resfl.sort() resfl.reverse() # using -log10 so larger is better - resfl = resfl[:topn] # truncate pvals = [x[0] for x in resfl] # need to scale resfl = [x[1] for x in resfl] # drop decoration + resfl = resfl[:topn] # truncate maxp = max(pvals) # need to scale minp = min(pvals) prange = abs(maxp-minp) + 0.5 # fudge scalefact = 1000.0/prange logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact)) for i,row in enumerate(resfl): - row[ppos] = '%d' % (int(scalefact*pvals[i])) + row[ppos] = '%d' % (int(scalefact*pvals[i])) resfl[i] = row # replace outf = file(outfname,'w') outf.write(header) --- a/tools/rgenetics/rgWebLogo3.xml Tue Apr 05 14:12:39 2011 -0400 +++ b/tools/rgenetics/rgWebLogo3.xml Tue Apr 05 14:14:32 2011 -0400 @@ -5,7 +5,7 @@ #if $range.mode == 'part' -l "$range.seqstart" -u "$range.seqend" #end if - </command> + </command><inputs><page><param format="fasta" name="input" type="data" label="Fasta File" /> @@ -71,7 +71,7 @@ <param name = "mode" value="complete" /><param name = "size" value="medium" /><param name = "colours" value="auto" /> - <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" /> + <output name="output" file="rgWebLogo3_test.jpg" ftype="jpg" compare="sim_size" delta="10000" /></test></tests> @@ -90,6 +90,15 @@ ---- +**Warning about input Fasta format files** + +The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. + +Fasta alignments from the companion ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file +a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta +sequences are the same length! + +---- **Attribution** http://bitbucket.org/galaxy/galaxy-central/changeset/79021bb57c1f/ changeset: r5348:79021bb57c1f user: jgoecks date: 2011-04-05 20:16:26 summary: Merge. affected #: 1 file (207 bytes) --- a/tool_conf.xml.main Tue Apr 05 14:14:32 2011 -0400 +++ b/tool_conf.xml.main Tue Apr 05 14:16:26 2011 -0400 @@ -169,6 +169,12 @@ <!-- <tool file="hyphy/hyphy_dnds_wrapper.xml" /> --><tool file="evolution/mutate_snp_codon.xml" /></section> + <section name="Motif Tools" id="motifs"> + <tool file="rgenetics/rgWebLogo3.xml" /> + </section> + <section name="Multiple Alignments" id="clustal"> + <tool file="rgenetics/rgClustalw.xml" /> + </section><section name="Metagenomic analyses" id="tax_manipulation"><tool file="taxonomy/gi2taxonomy.xml" /><tool file="taxonomy/t2t_report.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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