2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6f1d1bcb0b9c/ changeset: r5260:6f1d1bcb0b9c user: fubar date: 2011-03-23 22:18:29 summary: Fixes to clustalw tool - need a python wrapper to take care of Clustalw's bad habit of writing to an output path determined from the input path - naughty..Also added the dendrogram to the log output so test output sample updated; version bumped affected #: 1 file (34 bytes) --- a/tools/rgenetics/rgClustalw.xml Wed Mar 23 16:42:14 2011 -0400 +++ b/tools/rgenetics/rgClustalw.xml Wed Mar 23 17:18:29 2011 -0400 @@ -1,21 +1,22 @@ <tool id="clustalw" name="ClustalW" version="0.1"><description>multiple sequence alignment program for DNA or proteins</description> - <command> + <command interpreter="python"> + rgClustalw.py -i "$input" -o "$output" -s "$out_order" -l "$outlog" -t "$outname" -d "$dnarna" #if ($range.mode=="part") - clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order -RANGE=$range.seq_range_start,$range.seq_range_end - #elif ($range.mode=="complete") - clustalw2 -infile=$input -outfile=$output -OUTORDER=$out_order +-b "$range.seq_range_start" -e "$range.seq_range_end" #end if #if ($outcontrol.outform=="clustal") - -SEQNOS=$outcontrol.out_seqnos +-f "CLUSTAL" + #end if + #if ($outcontrol.outform=="clustal" and $outcontrol.out_seqnos=="ON") +-q "ON" #end if #if ($outcontrol.outform=="phylip") - -OUTPUT=PHYLIP +-f "PHYLIP" #end if #if ($outcontrol.outform=="fasta") - -OUTPUT=FASTA +-f "FASTA" #end if - -TYPE=$dnarna 1>$outlog 2>&1 </command><inputs><page> http://bitbucket.org/galaxy/galaxy-central/changeset/72f60642853b/ changeset: r5261:72f60642853b user: fubar date: 2011-03-23 22:20:47 summary: test data updated for clustalw test affected #: 1 file (664 bytes) --- a/test-data/rgClustal_testout.log Wed Mar 23 17:18:29 2011 -0400 +++ b/test-data/rgClustal_testout.log Wed Mar 23 17:20:47 2011 -0400 @@ -87,7 +87,7 @@ Sequences (10:11) Aligned. Score: 64 Sequences (10:12) Aligned. Score: 76 Sequences (11:12) Aligned. Score: 46 -Guide tree file created: [/share/shared/galaxy/database/files/002/dataset_2705.dnd] +Guide tree file created: [infile_copy.dnd] There are 11 groups Start of Multiple Alignment @@ -105,8 +105,40 @@ Group 10: Sequences: 4 Score:945 Group 11: Sequences: 12 Score:380 Alignment Score 6283 -firstres = 1 lastres = 63 -FASTA file created! -Fasta-Alignment file created [/share/shared/galaxy/database/files/002/dataset_2726.dat] +CLUSTAL-Alignment file created [/share/shared/galaxy/database/files/002/dataset_2801.dat] + +Clustal created the following dnd file for your information: +( +( +c_briggsae-chrII_+_/43862-46313:0.07349, +c_brenneri-Cbre_Contig60_+_/627772-630087:0.04317) +:0.02387, +( +c_remanei-Crem_Contig172_-_/123228-124941:0.06114, +c_elegans-II_+_/9706834-9708803:0.07219) +:0.01779, +( +( +( +c_briggsae-chrIfooI_+_/43862-46313:0.10368, +c_brenneri-Cbre_Contig60gak_+_/627772-630087:0.06298) +:0.01654, +( +c_remanei-Crem_Contig172foo_-_/123228-124941:0.05765, +c_elegans-II_+_more/9706834-9708803:0.05902) +:0.06262) +:0.31533, +( +( +c_briggsae-chrII_+_bar/43862-46313:0.02327, +c_brenneri-Cbre_Contig60fee_+_/627772-630087:0.13463) +:0.05016, +( +c_remanei-Crem_Contig172zot_-_/123228-124941:0.11667, +c_elegans-II_+_meh/9706834-9708803:0.11737) +:0.12013) +:0.20951) +:0.30133); + 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.