From 87ce8bd4b4a951bf78ce241e132088dbf5e9454f Mon Sep 17 00:00:00 2001 From: Chinmay Rao Date: Mon, 17 Dec 2007 14:02:48 +0000 Subject: [PATCH] Committing EMBOSS v5 tools: epestfind, est2genome extractseq freak fuzzpro garnier geecee --- tools/emboss_5/emboss_epestfind.xml | 64 ++++++++++++++ tools/emboss_5/emboss_est2genome.xml | 102 ++++++++++++++++++++++ tools/emboss_5/emboss_extractfeat.xml | 95 ++++++++++++++++++++ tools/emboss_5/emboss_extractseq.xml | 67 ++++++++++++++ tools/emboss_5/emboss_format_corrector.py | 50 +++++++++++ tools/emboss_5/emboss_freak.xml | 35 ++++++++ tools/emboss_5/emboss_fuzzpro.xml | 43 +++++++++ tools/emboss_5/emboss_garnier.xml | 57 ++++++++++++ tools/emboss_5/emboss_geecee.xml | 23 +++++ 9 files changed, 536 insertions(+) create mode 100644 tools/emboss_5/emboss_epestfind.xml create mode 100644 tools/emboss_5/emboss_est2genome.xml create mode 100644 tools/emboss_5/emboss_extractfeat.xml create mode 100644 tools/emboss_5/emboss_extractseq.xml create mode 100644 tools/emboss_5/emboss_format_corrector.py create mode 100644 tools/emboss_5/emboss_freak.xml create mode 100644 tools/emboss_5/emboss_fuzzpro.xml create mode 100644 tools/emboss_5/emboss_garnier.xml create mode 100644 tools/emboss_5/emboss_geecee.xml diff --git a/tools/emboss_5/emboss_epestfind.xml b/tools/emboss_5/emboss_epestfind.xml new file mode 100644 index 00000000000..7186c866270 --- /dev/null +++ b/tools/emboss_5/emboss_epestfind.xml @@ -0,0 +1,64 @@ + + Finds PEST motifs as potential proteolytic cleavage sites + emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor + -invalid $invalid -map $map -graph png -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_est2genome.xml b/tools/emboss_5/emboss_est2genome.xml new file mode 100644 index 00000000000..6a24dc1696f --- /dev/null +++ b/tools/emboss_5/emboss_est2genome.xml @@ -0,0 +1,102 @@ + + Align EST and genomic DNA sequences + est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty + $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +The input dataset needs to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html + + diff --git a/tools/emboss_5/emboss_extractfeat.xml b/tools/emboss_5/emboss_extractfeat.xml new file mode 100644 index 00000000000..dbbae6fe3b7 --- /dev/null +++ b/tools/emboss_5/emboss_extractfeat.xml @@ -0,0 +1,95 @@ + + + Extract features from a sequence + extractfeat -sequence $input1 -outseq $out_file1 -before $before -after $after -source "$source" -type "$type" -sense $sense -minscore $minscore -maxscore $maxscore -tag "$tag" -value + "$value" -join $join -featinname $featinname -describe "$describe" -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_extractseq.xml b/tools/emboss_5/emboss_extractseq.xml new file mode 100644 index 00000000000..07d8c781597 --- /dev/null +++ b/tools/emboss_5/emboss_extractseq.xml @@ -0,0 +1,67 @@ + + Extract regions from a sequence + extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractseq.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_format_corrector.py b/tools/emboss_5/emboss_format_corrector.py new file mode 100644 index 00000000000..a9b83ad7fde --- /dev/null +++ b/tools/emboss_5/emboss_format_corrector.py @@ -0,0 +1,50 @@ +#EMBOSS format corrector + +import operator +#from galaxy import datatypes + +#Properly set file formats after job run +def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr): +#Properly set file formats before job run +#def exec_before_job(trans, inp_data, out_data, param_dict,tool): + #why isn't items an ordered list? + items = out_data.items() + #lets sort it ourselves.... + items = sorted(items, key=operator.itemgetter(0)) + #items is now sorted... + + #normal filetype correction + data_count=1 + for name, data in items: + outputType = param_dict.get( 'out_format'+str(data_count), None ) + #print "data_count",data_count, "name", name, "outputType", outputType + if outputType !=None: + if outputType == 'ncbi': + outputType = "fasta" + elif outputType == 'excel': + outputType = "tabular" + elif outputType == 'text': + outputType = "txt" + data = app.datatypes_registry.change_datatype(data, outputType) + data.flush() + data_count+=1 + + #html filetype correction + data_count=1 + for name, data in items: + wants_plot = param_dict.get( 'html_out'+str(data_count), None ) + ext = "html" + if wants_plot == "yes": + data = app.datatypes_registry.change_datatype(data, ext) + data.flush() + data_count+=1 + + #png file correction + data_count=1 + for name, data in items: + wants_plot = param_dict.get( 'plot'+str(data_count), None ) + ext = "png" + if wants_plot == "yes": + data = app.datatypes_registry.change_datatype(data, ext) + data.flush() + data_count+=1 diff --git a/tools/emboss_5/emboss_freak.xml b/tools/emboss_5/emboss_freak.xml new file mode 100644 index 00000000000..494997c603a --- /dev/null +++ b/tools/emboss_5/emboss_freak.xml @@ -0,0 +1,35 @@ + + Residue/base frequency table or plot + freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_fuzzpro.xml b/tools/emboss_5/emboss_fuzzpro.xml new file mode 100644 index 00000000000..1e6e55f5240 --- /dev/null +++ b/tools/emboss_5/emboss_fuzzpro.xml @@ -0,0 +1,43 @@ + + Protein pattern search + fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -mismatch $mismatch -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_garnier.xml b/tools/emboss_5/emboss_garnier.xml new file mode 100644 index 00000000000..e6134416955 --- /dev/null +++ b/tools/emboss_5/emboss_garnier.xml @@ -0,0 +1,57 @@ + + Predicts protein secondary structure + garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_geecee.xml b/tools/emboss_5/emboss_geecee.xml new file mode 100644 index 00000000000..f101faa11cf --- /dev/null +++ b/tools/emboss_5/emboss_geecee.xml @@ -0,0 +1,23 @@ + + Calculates fractional GC content of nucleic acid sequences + geecee -sequence $input1 -outfile $out_file1 -auto + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/geecee.html + + \ No newline at end of file