# HG changeset patch # User iuc # Date 1485800860 18000 # Node ID 0e2484b6829b3fac218acc614b142349096e911b # Parent 9b98d3d903c6fccfafefc6a80d012d4e9e005d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68 diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_antigenic.xml --- a/emboss_antigenic.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_antigenic.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,36 +1,35 @@ - - Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. - emboss - antigenic -sequence $input1 -outfile $out_file1 -minlen $minlen -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - + + Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. + + macros.xml + + + + antigenic -sequence '$input1' -outfile '$out_file1' -minlen $minlen -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + - - - - - + + + + + @@ -39,20 +38,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/antigenic.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ - + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/antigenic.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_backtranseq.xml --- a/emboss_backtranseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_backtranseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,200 +1,200 @@ - - Back translate a protein sequence - emboss - backtranseq -sequence $input1 -outfile $out_file1 -cfile $cfile -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Back translate a protein sequence + + macros.xml + + + + backtranseq -sequence '$input1' -outfile '$out_file1' -cfile $cfile -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -203,26 +203,17 @@ - - + +.. class:: warningmark -.. class:: warningmark +The input dataset needs to be sequences. -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/backtranseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/backtranseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_banana.pl --- a/emboss_banana.pl Fri Aug 12 19:17:10 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ -#! /usr/bin/perl -w -use strict; - -my $cmd_string = join (" ",@ARGV); -#my $cmd_string = "/home/djb396/temp/emboss/bin/banana -sequence /home/djb396/universe-prototype/test.fasta -outfile result.txt -graph png -goutfile results -auto"; -my $results = `$cmd_string`; -my @files = split("\n",$results); -foreach my $thisLine (@files) -{ - if ($thisLine =~ /Created /i) - { - $thisLine =~ /[\w|\.]+$/; - $thisLine =$&; - print "outfile: $thisLine\n"; - } -} diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_banana.xml --- a/emboss_banana.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_banana.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,32 +1,26 @@ - - Bending and curvature plot in B-DNA - emboss - banana -sequence $input1 -outfile $out_file1 -graph none -auto - - - - - - - + + Bending and curvature plot in B-DNA + + macros.xml + + + banana -sequence '$input1' -outfile '$out_file1' -graph none -auto + + + + + - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/banana.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/banana.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_biosed.xml --- a/emboss_biosed.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_biosed.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,52 +1,49 @@ - - Replace or delete sequence sections - emboss - biosed -sequence $input1 -outseq $out_file1 -target "$target" -replace "$replace" -osformat2 "$out_format1" -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Replace or delete sequence sections + + macros.xml + + + + biosed -sequence '$input1' -outseq '$out_file1' -target '$target' -replace '$replace' -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -56,10 +53,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -67,15 +62,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/biosed.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/biosed.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_btwisted.xml --- a/emboss_btwisted.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_btwisted.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,32 +1,26 @@ - - Calculates the twisting in a B-DNA sequence - emboss - btwisted -sequence $input1 -outfile $out_file1 -auto - - - - - - - + + Calculates the twisting in a B-DNA sequence + + macros.xml + + + btwisted -sequence '$input1' -outfile '$out_file1' -auto + + + + + - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/btwisted.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/btwisted.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_cai.xml --- a/emboss_cai.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_cai.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,193 +1,186 @@ - - CAI codon adaptation index - emboss - cai -seqall '$input1' -outfile '$out_file1' -cfile '$cfile' -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/cai.html - ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ - - + + CAI codon adaptation index + + macros.xml + + + cai -seqall '$input1' -outfile '$out_file1' -cfile $cfile -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +The input dataset needs to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cai.html + + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_cai_custom.xml --- a/emboss_cai_custom.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_cai_custom.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,18 +1,17 @@ - - CAI codon adaptation index using custom codon usage file - emboss - cai -seqall $input1 -outfile $out_file1 -cfile $input2 -auto - - - - - - - - - - - + + CAI codon adaptation index using custom codon usage file + + macros.xml + + + cai -seqall '$input1' -outfile '$out_file1' -cfile '$input2' -auto + + + + + + + .. class:: warningmark @@ -21,15 +20,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cai_custom.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cai.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_chaos.xml --- a/emboss_chaos.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_chaos.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,31 +1,25 @@ - - Create a chaos game representation plot for a sequence - emboss - emboss_single_outputfile_wrapper.pl chaos -sequence $input1 -graph png -goutfile $out_file1 -auto - - - - - - - + + Create a chaos game representation plot for a sequence + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' chaos -sequence '$input1' -graph png -goutfile '$out_file1' -auto + + + + + + --> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chaos.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/chaos.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_charge.xml --- a/emboss_charge.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_charge.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,17 +1,16 @@ - - Protein charge plot - emboss - charge -seqall $input1 -outfile $out_file1 -window $window -auto - - - - - - - - - - + + Protein charge plot + + macros.xml + + + charge -seqall '$input1' -outfile '$out_file1' -window $window -auto + + + + + + + --> +.. class:: warningmark -.. class:: warningmark +The input dataset needs to be sequences. -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/charge.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/charge.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_checktrans.xml --- a/emboss_checktrans.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_checktrans.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,63 +1,59 @@ - - Reports STOP codons and ORF statistics of a protein - emboss - checktrans -sequence $input1 -outfile $out_file1 -outseq $out_file2 -osformat3 $out_format2 -outfeat $out_file3 -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Reports STOP codons and ORF statistics of a protein + + macros.xml + + + + checktrans -sequence '$input1' -outfile '$out_file1' -outseq '$out_file2' -osformat3 $out_format2 -outfeat '$out_file3' -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + --> +.. class:: warningmark -.. class:: warningmark +The input dataset needs to be sequences. -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/checktrans.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/checktrans.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_chips.xml --- a/emboss_chips.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_chips.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,19 +1,19 @@ - - Codon usage statistics - emboss - chips -seqall $input1 -outfile $out_file1 -sum $sum -auto - - - - - - - - - - - - + + Codon usage statistics + + macros.xml + + + chips -seqall '$input1' -outfile '$out_file1' -sum $sum -auto + + + + + + + + + @@ -21,18 +21,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chips.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/chips.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_cirdna.xml --- a/emboss_cirdna.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_cirdna.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,31 +1,25 @@ - - Draws circular maps of DNA constructs - emboss - emboss_single_outputfile_wrapper.pl cirdna -infile $input1 -graphout png -goutfile $out_file1 -auto - - - - - - - + + Draws circular maps of DNA constructs + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' cirdna -infile '$input1' -graphout png -goutfile '$out_file1' -auto + + + + + + --> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cirdna.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cirdna.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_codcmp.xml --- a/emboss_codcmp.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_codcmp.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,319 +1,320 @@ - - Codon usage table comparison - emboss - codcmp -first $cfile1 -second $cfile2 -outfile $out_file1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Codon usage table comparison + + macros.xml + + + codcmp -first $cfile1 -second $cfile2 -outfile '$out_file1' -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -321,18 +322,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/codcmp.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/codcmp.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_coderet.xml --- a/emboss_coderet.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_coderet.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,81 +1,70 @@ - - Extract CDS, mRNA and translations from feature tables - emboss - - coderet -seqall $input1 -outfile $out_file1 -auto - - - - - - - - + + Extract CDS, mRNA and translations from feature tables + + macros.xml + + + + + coderet -seqall '$input1' -outfile '$out_file1' -auto + + + + + + - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/coderet.html - + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_compseq.xml --- a/emboss_compseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_compseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,24 +1,22 @@ - - Count composition of dimer/trimer/etc words in a sequence - emboss - compseq -sequence $input1 -outfile $out_file1 -word $word -frame $frame -auto - - - - - - - - - - - - - - - - - + + Count composition of dimer/trimer/etc words in a sequence + + macros.xml + + + compseq -sequence '$input1' -outfile '$out_file1' -word $word -frame $frame -auto + + + + + + + + + + + + @@ -27,7 +25,7 @@ - + .. class:: warningmark @@ -36,15 +34,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/compseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/compseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_cpgplot.xml --- a/emboss_cpgplot.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_cpgplot.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,41 +1,27 @@ - - Plot CpG rich areas - emboss - emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto - - - - - - - - - - - - - - - - - - - - - - - + + Plot CpG rich areas + + macros.xml + + + + perl '$__tool_directory__/emboss_cpgplot_wrapper.pl' cpgplot -sequence '$input1' -window $window -minlen $minlen -minpc $minpc -outfile '$outfile' -graph png -goutfile '$goutfile' -outfeat '$outfeat' -minoe $minoe -auto + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cpgplot.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_cpgreport.xml --- a/emboss_cpgreport.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_cpgreport.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,65 +1,57 @@ - - Reports all CpG rich regions - emboss - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. 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/cpgreport.html - ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ - - + + Reports all CpG rich regions + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +The input dataset needs to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cpgreport.html + + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_cusp.xml --- a/emboss_cusp.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_cusp.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,21 +1,22 @@ - - Create a codon usage table - emboss - cusp -sequence $input1 -outfile $out_file1 -auto - - - - - - - + + Create a codon usage table + + macros.xml + + + cusp -sequence '$input1' -outfile '$out_file1' -auto + + + + + - + .. class:: warningmark @@ -24,15 +25,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cusp.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cusp.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_cutseq.xml --- a/emboss_cutseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_cutseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,52 +1,49 @@ - - Removes a specified section from a sequence - emboss - cutseq -sequence $input1 -outseq $out_file1 -from $from -to $to -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Removes a specified section from a sequence + + macros.xml + + + + cutseq -sequence '$input1' -outseq '$out_file1' -from $from -to $to -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -56,8 +53,7 @@ - - + .. class:: warningmark @@ -66,15 +62,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cutseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cutseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_dan.xml --- a/emboss_dan.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_dan.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,60 +1,42 @@ - - Calculates DNA RNA/DNA melting temperature - emboss - emboss_single_outputfile_wrapper.pl dan -sequence $input1 -windowsize $window -goutfile $out_file1 -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc - -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Calculates DNA RNA/DNA melting temperature + + macros.xml + + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dan -sequence '$input1' -windowsize $window -goutfile '$out_file1' -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc + -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + --> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dan.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_degapseq.xml --- a/emboss_degapseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_degapseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,46 +1,47 @@ - - Removes gap characters from sequences - emboss - degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Removes gap characters from sequences + + macros.xml + + + + degapseq -sequence '$input1' -outseq '$out_file1' -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -48,19 +49,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/degapseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/degapseq.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_descseq.xml --- a/emboss_descseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_descseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,57 +1,53 @@ - - Alter the name or description of a sequence - emboss - descseq -sequence $input1 -outseq $out_file1 -name "$seqname" -description "$desc" -append $append -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Alter the name or description of a sequence + + macros.xml + + + + descseq -sequence '$input1' -outseq '$out_file1' -name '$seqname' -description '$desc' -append $append -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -62,19 +58,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/descseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/descseq.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_diffseq.xml --- a/emboss_diffseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_diffseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,72 +1,58 @@ - - Find differences between nearly identical sequences - emboss - diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 - $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Find differences between nearly identical sequences + + macros.xml + + + + diffseq -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -globaldifferences $globaldifferences -rformat3 + $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/diffseq.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_digest.xml --- a/emboss_digest.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_digest.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,73 +1,61 @@ - - Protein proteolytic enzyme or reagent cleavage digest - emboss - digest -seqall $input1 -outfile $out_file1 -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Protein proteolytic enzyme or reagent cleavage digest + + macros.xml + + + + digest -seqall '$input1' -outfile '$out_file1' -menu $menu -unfavoured $unfavoured -overlap $overlap -allpartials $allpartials -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/digest.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/digest.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_dotmatcher.xml --- a/emboss_dotmatcher.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_dotmatcher.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,37 +1,24 @@ - - Displays a thresholded dotplot of two sequences - emboss - emboss_single_outputfile_wrapper.pl dotmatcher -asequence $input1 -bsequence $input2 -goutfile $out_file1 -windowsize $windowsize -threshold $threshold -graph png -xygraph png - -auto - - - - - - - - - - - - - - - - + + Displays a thresholded dotplot of two sequences + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dotmatcher -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -windowsize $windowsize -threshold $threshold -graph png -xygraph png -auto + + + + + + + + - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotmatcher.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dotmatcher.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_dotpath.xml --- a/emboss_dotpath.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_dotpath.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,44 +1,31 @@ - - Non-overlapping wordmatch dotplot of two sequences - emboss - emboss_single_outputfile_wrapper.pl dotpath -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png - -auto - - - - - - - - - - - - - - - - - - - - - - - + + Non-overlapping wordmatch dotplot of two sequences + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dotpath -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize $wordsize -overlaps $overlaps -boxit $boxit -graph png -auto + + + + + + + + + + + + + + + - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dotpath.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dotpath.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_dottup.xml --- a/emboss_dottup.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_dottup.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,38 +1,27 @@ - - Displays a wordmatch dotplot of two sequences - emboss - emboss_single_outputfile_wrapper.pl dottup -asequence $input1 -bsequence $input2 -goutfile $out_file1 -wordsize $wordsize -boxit $boxit -graph png -xygraph png -auto - - - - - - - - - - - - - - - - - - + + Displays a wordmatch dotplot of two sequences + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dottup -asequence '$input1' -bsequence '$input2' -goutfile '$out_file1' -wordsize $wordsize -boxit $boxit -graph png -xygraph png -auto + + + + + + + + + + + - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dottup.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dottup.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_dreg.xml --- a/emboss_dreg.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_dreg.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,30 +1,22 @@ - - Regular expression search of a nucleotide sequence - emboss - dreg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto - - - - - - - - - - + + Regular expression search of a nucleotide sequence + + macros.xml + + + dreg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -raccshow3 "no" -rusashow3 "no" -rdesshow3 "no" -auto + + + + + + - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/dreg.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dreg.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_einverted.xml --- a/emboss_einverted.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_einverted.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,29 +1,20 @@ - - Finds DNA inverted repeats - emboss - einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto - - - - - - - - - - - - - - - - - - - - - - + + Finds DNA inverted repeats + + macros.xml + + + einverted -sequence '$input1' -outfile '$out_file1' -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto + + + + + + + + + + @@ -35,7 +26,7 @@ - + .. class:: warningmark @@ -44,15 +35,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/einverted.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_epestfind.xml --- a/emboss_epestfind.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_epestfind.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,48 +1,40 @@ - - Finds PEST motifs as potential proteolytic cleavage sites - emboss - emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor - -invalid $invalid -map $map -graph png -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds PEST motifs as potential proteolytic cleavage sites + + macros.xml + + + perl '$__tool_directory__/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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + output file contains file location info --> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/epestfind.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_equicktandem.xml --- a/emboss_equicktandem.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_equicktandem.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,40 +1,37 @@ - - Finds tandem repeats - emboss - equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds tandem repeats + + macros.xml + + + + equicktandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -44,8 +41,7 @@ - - + .. class:: warningmark @@ -54,15 +50,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/equicktandem.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_est2genome.xml --- a/emboss_est2genome.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_est2genome.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,71 +1,47 @@ - - Align EST and genomic DNA sequences - emboss - 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 $width -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Align EST and genomic DNA sequences + + macros.xml + + + est2genome -estsequence '$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 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -88,7 +64,7 @@ - + .. class:: warningmark @@ -97,15 +73,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/est2genome.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_etandem.xml --- a/emboss_etandem.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_etandem.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,53 +1,46 @@ - - Looks for tandem repeats in a nucleotide sequence - emboss - etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Looks for tandem repeats in a nucleotide sequence + + macros.xml + + + + etandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -60,8 +53,7 @@ - - + .. class:: warningmark @@ -70,17 +62,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/etandem.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/etandem.html + - - diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_extractfeat.xml --- a/emboss_extractfeat.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_extractfeat.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,58 +1,38 @@ - - - Extract features from a sequence - emboss - 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 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + Extract features from a sequence + + macros.xml + + + + extractfeat -sequence '$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 + + + + + + + + + + + + + + + + + + + + + + + + + @@ -81,24 +61,16 @@ - - - - - - - + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractfeat.html ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/extractfeat.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_extractseq.xml --- a/emboss_extractseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_extractseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,54 +1,52 @@ - - Extract regions from a sequence - emboss - extractseq -sequence $input1 -outseq $out_file1 -regions $regions -separate $separate -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Extract regions from a sequence + + macros.xml + + + + extractseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -separate $separate -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -58,19 +56,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/extractseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/extractseq.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_format_corrector.py --- a/emboss_format_corrector.py Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_format_corrector.py Mon Jan 30 13:27:40 2017 -0500 @@ -1,21 +1,18 @@ -#EMBOSS format corrector - +# EMBOSS format corrector import operator -#Properly set file formats before job run + +# Properly set file formats before job run def exec_before_job( app, inp_data=None, out_data=None, tool=None, param_dict=None ): - #why isn't items an ordered list? + # 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 + + # 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: + outputType = param_dict.get( 'out_format' + str(data_count), None ) + if outputType is not None: if outputType == 'ncbi': outputType = "fasta" elif outputType == 'excel': @@ -25,26 +22,26 @@ data = app.datatypes_registry.change_datatype(data, outputType) app.model.context.add( data ) app.model.context.flush() - data_count+=1 - - #html filetype correction - data_count=1 + 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 ) + 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) app.model.context.add( data ) app.model.context.flush() - data_count+=1 - - #png file correction - data_count=1 + data_count += 1 + + # png file correction + data_count = 1 for name, data in items: - wants_plot = param_dict.get( 'plot'+str(data_count), None ) + wants_plot = param_dict.get( 'plot' + str(data_count), None ) ext = "png" if wants_plot == "yes": data = app.datatypes_registry.change_datatype(data, ext) app.model.context.add( data ) app.model.context.flush() - data_count+=1 + data_count += 1 diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_freak.xml --- a/emboss_freak.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_freak.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,23 +1,18 @@ - - Residue/base frequency table or plot - emboss - freak -seqall $input1 -outfile $out_file1 -window $window -letters $letters -graph png -step $step -auto - - - - - - - - - - - - - - - - + + Residue/base frequency table or plot + + macros.xml + + + freak -seqall '$input1' -outfile '$out_file1' -window $window -letters '$letters' -graph png -step $step -auto + + + + + + + + @@ -27,18 +22,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/freak.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/freak.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_fuzznuc.xml --- a/emboss_fuzznuc.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_fuzznuc.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,53 +1,50 @@ - - Nucleic acid pattern search - emboss - fuzznuc -sequence $input1 -outfile $out_file1 -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Nucleic acid pattern search + + macros.xml + + + + fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - + + + + + + + + @@ -58,10 +55,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -69,15 +64,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzznuc.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_fuzzpro.xml --- a/emboss_fuzzpro.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_fuzzpro.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,60 +1,50 @@ - - Protein pattern search - emboss - fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html - ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ - - + + Protein pattern search + + macros.xml + + + + fuzzpro -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzzpro.html + + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_fuzztran.xml --- a/emboss_fuzztran.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_fuzztran.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,72 +1,67 @@ - - Protein pattern search after translation - emboss - fuzztran -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Protein pattern search after translation + + macros.xml + + + + fuzztran -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -frame $frame -table $table -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -78,10 +73,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -89,15 +82,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzztran.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzztran.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_garnier.xml --- a/emboss_garnier.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_garnier.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,45 +1,43 @@ - - Predicts protein secondary structure - emboss - garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Predicts protein secondary structure + + macros.xml + + + + garnier -sequence '$input1' -outfile '$out_file1' -idc $idc -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -48,19 +46,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: https://galaxy-iuc.github.io/emboss-5.0-docs/garnier.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_geecee.xml --- a/emboss_geecee.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_geecee.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,32 +1,26 @@ - - Calculates fractional GC content of nucleic acid sequences - emboss - geecee -sequence $input1 -outfile $out_file1 -auto - - - - - - - + + Calculates fractional GC content of nucleic acid sequences + + macros.xml + + + geecee -sequence '$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 - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/geecee.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_getorf.xml --- a/emboss_getorf.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_getorf.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,102 +1,92 @@ - - Finds and extracts open reading frames (ORFs) - emboss - getorf -sequence $input1 -outseq $out_file1 -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking - -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds and extracts open reading frames (ORFs) + + macros.xml + + + + getorf -sequence '$input1' -outseq '$out_file1' -table $table -minsize $minsize -maxsize $maxsize -find $find -methionine $methionine -circular $circular -reverse $reverse -flanking $flanking + -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -112,10 +102,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -123,15 +111,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/getorf.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_helixturnhelix.xml --- a/emboss_helixturnhelix.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_helixturnhelix.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,47 +1,41 @@ - - Report nucleic acid binding motifs - emboss - helixturnhelix -sequence $input1 -outfile $out_file1 -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Report nucleic acid binding motifs + + macros.xml + + + + helixturnhelix -sequence '$input1' -outfile '$out_file1' -mean $mean -sd $sd -minsd $minsd -eightyseven $eightyseven -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -53,19 +47,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/helixturnhelix.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/helixturnhelix.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_hmoment.xml --- a/emboss_hmoment.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_hmoment.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,20 +1,17 @@ - - Hydrophobic moment calculation - emboss - hmoment -seqall $input1 -outfile $out_file1 -window $window -aangle $aangle -graph png -auto - - - - - - - - - - - - - + + Hydrophobic moment calculation + + macros.xml + + + hmoment -seqall '$input1' -outfile '$out_file1' -window $window -aangle $aangle -graph png -auto + + + + + + + @@ -23,18 +20,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/hmoment.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/hmoment.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_iep.xml --- a/emboss_iep.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_iep.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,25 +1,21 @@ - - Calculates the isoelectric point of a protein - emboss - iep -sequence $input1 -outfile $out_file1 -step $step -amino $amino -graph png -termini $termini -auto - - - - - - - - - - - - - - - - - - + + Calculates the isoelectric point of a protein + + macros.xml + + + iep -sequence '$input1' -outfile '$out_file1' -step $step -amino $amino -graph png -termini $termini -auto + + + + + + + + + + + @@ -29,18 +25,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/iep.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/iep.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_infoseq.xml --- a/emboss_infoseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_infoseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,84 +1,67 @@ - + - Displays some simple information about sequences - emboss - infoseq -sequence $input1 -outfile $out_file1 -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc - $pgc -description $description -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Displays some simple information about sequences + + macros.xml + + + + infoseq -sequence '$input1' -outfile '$out_file1' -html $html_out1 -heading $heading -usa $usa -name $disname -accession $accession -gi $gi -version $version -type $type -length $length -pgc + $pgc -description $description -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/infoseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/infoseq.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_isochore.xml --- a/emboss_isochore.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_isochore.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,29 +1,25 @@ - + Plots isochores in large DNA sequences - emboss - emboss_single_outputfile_wrapper.pl isochore -sequence $input1 -outfile $ofile2 -goutfile $ofile1 -graph png -window $window -shift $shift -auto - + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' isochore -sequence '$input1' -outfile '$ofile2' -goutfile '$ofile1' -graph png -window $window -shift $shift -auto - - - - - - - - - + + + - - + + - .. class:: warningmark The input dataset needs to be sequences. @@ -43,9 +38,9 @@ **Syntax** -This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences. You can view the original documentation here_. +This application plots GC content over a sequence. It is intended for large sequences such as complete chromosomes or large genomic contigs, although interesting results can also be obtained from shorter sequences. You can view the original documentation here_. - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/isochore.html + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/isochore.html - Both **Window size** and **Shift increment** are intergers. @@ -77,14 +72,6 @@ - Output graphics file: .. image:: ./static/emboss_icons/isochore.png - ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ - + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_lindna.xml --- a/emboss_lindna.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_lindna.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,107 +1,72 @@ - + - Draws linear maps of DNA constructs - emboss - lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour - -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight - $rangeheight -gapgroup $gapgroup -postext $postext -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Draws linear maps of DNA constructs + + macros.xml + + + lindna -infile '$input1' -graphout png -goutfile '$out_file1' -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour + -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight + $rangeheight -gapgroup $gapgroup -postext $postext -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/lindna.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/lindna.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_marscan.xml --- a/emboss_marscan.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_marscan.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,33 +1,34 @@ - - Finds MAR/SAR sites in nucleic sequences - emboss - marscan -sequence $input1 -outfile $out_file1 -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds MAR/SAR sites in nucleic sequences + + macros.xml + + + + marscan -sequence '$input1' -outfile '$out_file1' -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + @@ -35,19 +36,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/marscan.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/marscan.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_maskfeat.xml --- a/emboss_maskfeat.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_maskfeat.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,57 +1,53 @@ - - Mask off features of a sequence - emboss - maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Mask off features of a sequence + + macros.xml + + + + maskfeat -sequence '$input1' -outseq '$out_file1' -type '$type' -tolower $tolower -maskchar '$maskchar' -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -62,19 +58,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskfeat.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/maskfeat.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_maskseq.xml --- a/emboss_maskseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_maskseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,57 +1,53 @@ - - Mask off regions of a sequence - emboss - maskseq -sequence $input1 -outseq $out_file1 -regions "$regions" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Mask off regions of a sequence + + macros.xml + + + + maskseq -sequence '$input1' -outseq '$out_file1' -regions '$regions' -tolower $tolower -maskchar '$maskchar' -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -62,19 +58,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/maskseq.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_matcher.xml --- a/emboss_matcher.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_matcher.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,41 +1,34 @@ - - Finds the best local alignments between two sequences - emboss - matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds the best local alignments between two sequences + + macros.xml + + + + matcher -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + @@ -47,19 +40,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/matcher.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_megamerger.xml --- a/emboss_megamerger.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_megamerger.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,71 +1,59 @@ - - Merge two large overlapping nucleic acid sequences - emboss - megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Merge two large overlapping nucleic acid sequences + + macros.xml + + + + megamerger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/megamerger.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/megamerger.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_merger.xml --- a/emboss_merger.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_merger.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,84 +1,70 @@ - - Merge two overlapping nucleic acid sequences - emboss - merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Merge two overlapping nucleic acid sequences + + macros.xml + + + + merger -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -outfile '$out_file2' -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/merger.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_msbar.xml --- a/emboss_msbar.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_msbar.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,91 +1,82 @@ - - Mutate sequence beyond all recognition - emboss - msbar -sequence $input1 -outseq $out_file1 -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1 - -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Mutate sequence beyond all recognition + + macros.xml + + + + msbar -sequence '$input1' -outseq '$out_file1' -count $count -point $point -block $block -codon $codon -inframe $inframe -minimum $minimum -maximum $maximum -osformat2 $out_format1 + -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -100,10 +91,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -111,15 +100,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/msbar.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/msbar.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_needle.xml --- a/emboss_needle.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_needle.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,43 +1,37 @@ - - Needleman-Wunsch global alignment - emboss - needle -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Needleman-Wunsch global alignment + + macros.xml + + + + needle -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + - - - - + + + + @@ -49,10 +43,8 @@ - - + - .. class:: warningmark needle reads any two sequences of the same type (DNA or protein). @@ -61,7 +53,7 @@ **Syntax** -This tool uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length. +This tool uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length. - **Optimal alignment:** Dynamic programming methods ensure the optimal global alignment by exploring all possible alignments and choosing the best. @@ -72,8 +64,8 @@ - **Gap extension penalty:** [0.5 for any sequence] The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. (Floating point number from 0.0 to 10.0) You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/needle.html + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/needle.html ----- @@ -85,7 +77,7 @@ TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTG -- If both Sequence1 and Sequence2 take the above file as input, Gap open penalty equals 10.0, Gap extension penalty equals 0.5, Brief identity and similarity is set to Yes, Output Alignment File Format is set to SRS pairs, the output file is:: +- If both Sequence1 and Sequence2 take the above file as input, Gap open penalty equals 10.0, Gap extension penalty equals 0.5, Brief identity and similarity is set to Yes, Output alignment file format is set to SRS pairs, the output file is:: ######################################## # Program: needle @@ -93,7 +85,7 @@ # Align_format: srspair # Report_file: ./database/files/dataset_7.dat ######################################## - + #======================================= # # Aligned_sequences: 2 @@ -114,21 +106,13 @@ hg18_dna 1 TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA 50 |||||||||||||||||||||||||||||||||||||||||||||||||| hg18_dna 1 TTTATGTCTATAATCCTTACCAAAAGTTACCTTGGAATAAGAAGAAGTCA 50 - + hg18_dna 51 GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTG 83 ||||||||||||||||||||||||||||||||| hg18_dna 51 GTAAAAAGAAGGCTGTTGTTCCGTGAAATACTG 83 - + #--------------------------------------- #--------------------------------------- - - ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_newcpgreport.xml --- a/emboss_newcpgreport.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_newcpgreport.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,29 +1,20 @@ - - Report CpG rich areas - emboss - newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto - - - - - - - - - - - - - - - - - - - - - - + + Report CpG rich areas + + macros.xml + + + newcpgreport -sequence '$input1' -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile '$out_file1' -minoe $minoe -auto + + + + + + + + + + @@ -35,18 +26,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/newcpgreport.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_newcpgseek.xml --- a/emboss_newcpgseek.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_newcpgseek.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,17 +1,16 @@ - - Reports CpG rich region - emboss - newcpgseek -sequence $input1 -outfile $out_file1 -score $score -auto - - - - - - - - - - + + Reports CpG rich region + + macros.xml + + + newcpgseek -sequence '$input1' -outfile '$out_file1' -score $score -auto + + + + + + @@ -19,9 +18,8 @@ - + - .. class:: warningmark The input dataset needs to be sequences. @@ -29,15 +27,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgseek.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/newcpgseek.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_newseq.xml --- a/emboss_newseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_newseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,91 +1,79 @@ - - Type in a short new sequence - emboss - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newseq.html - ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ - - + + Type in a short new sequence + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/newseq.html + + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_noreturn.xml --- a/emboss_noreturn.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_noreturn.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,20 +1,20 @@ - - Removes carriage return from ASCII files - emboss - noreturn -infile $input1 -outfile $out_file1 -system $system -auto - - - - - - - - - - - - - + + Removes carriage return from ASCII files + + macros.xml + + + noreturn -infile '$input1' -outfile '$out_file1' -system $system -auto + + + + + + + + + + @@ -22,18 +22,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/noreturn.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/noreturn.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_notseq.xml --- a/emboss_notseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_notseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,49 +1,48 @@ - - Exclude a set of sequences and write out the remaining ones - emboss - notseq -sequence $input1 -outseq $out_file1 -exclude "$exclude" -osformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Exclude a set of sequences and write out the remaining ones + + macros.xml + + + + notseq -sequence '$input1' -outseq '$out_file1' -exclude '$exclude' -osformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -52,10 +51,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -63,15 +60,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/notseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/notseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_nthseq.xml --- a/emboss_nthseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_nthseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,49 +1,48 @@ - - Writes one sequence from a multiple set of sequences - emboss - nthseq -sequence $input1 -outseq $out_file1 -number $number -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Writes one sequence from a multiple set of sequences + + macros.xml + + + + nthseq -sequence '$input1' -outseq '$out_file1' -number $number -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -52,10 +51,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -63,15 +60,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/nthseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/nthseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_octanol.xml --- a/emboss_octanol.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_octanol.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,46 +1,35 @@ - - - Displays protein hydropathy - emboss - emboss_single_outputfile_wrapper.pl octanol -sequence $input1 -graph png -goutfile $out_file1 -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot - -differenceplot $differenceplot -auto - - - - - - - - - - - - - - - - - - - - - - - - - - + + + Displays protein hydropathy + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' octanol -sequence '$input1' -graph png -goutfile '$out_file1' -width $width -octanolplot $octanolplot -interfaceplot $interfaceplot + -differenceplot $differenceplot -auto + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/octanol.html ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/octanol.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_oddcomp.xml --- a/emboss_oddcomp.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_oddcomp.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,27 +1,22 @@ - + - Find protein sequence regions with a biased composition - emboss - oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto - - - - - - - - - - - - - - - - - - + Find protein sequence regions with a biased composition + + macros.xml + + + oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window $window -ignorebz $ignorebz -auto + + + + + + + + + + + + --> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/oddcomp.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_palindrome.xml --- a/emboss_palindrome.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_palindrome.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,31 +1,23 @@ - - Looks for inverted repeats in a nucleotide sequence - emboss - palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto - - - - - - - - - - - - - - - - - - - - - - - - + + Looks for inverted repeats in a nucleotide sequence + + macros.xml + + + palindrome -sequence '$input1' -outfile '$out_file1' -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto + + + + + + + + + + + + + @@ -37,9 +29,8 @@ - + - .. class:: warningmark The input dataset needs to be sequences. @@ -47,15 +38,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/palindrome.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pasteseq.xml --- a/emboss_pasteseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pasteseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,52 +1,49 @@ - - Insert one sequence into another - emboss - pasteseq -asequence $input2 -bsequence $input1 -outseq $out_file1 -pos $pos -osformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Insert one sequence into another + + macros.xml + + + + pasteseq -asequence '$input2' -bsequence '$input1' -outseq '$out_file1' -pos $pos -osformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -56,10 +53,8 @@ - - + - .. class:: warningmark The input datasets need to be sequences. @@ -67,15 +62,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pasteseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pasteseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_patmatdb.xml --- a/emboss_patmatdb.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_patmatdb.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,36 +1,35 @@ - - Search a protein sequence with a motif - emboss - patmatdb -sequence $input1 -outfile $out_file1 -motif "$motif" -rformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Search a protein sequence with a motif + + macros.xml + + + + patmatdb -sequence '$input1' -outfile '$out_file1' -motif '$motif' -rformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + @@ -39,19 +38,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/patmatdb.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/patmatdb.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pepcoil.xml --- a/emboss_pepcoil.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepcoil.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,32 +1,28 @@ - - Predicts coiled coil regions - emboss - pepcoil -sequence $input1 -outfile $out_file1 -window $window -coil $coil -frame $frame -other $other -auto - - - - - - - - - - - - - - - - - - - - - - - - - + + Predicts coiled coil regions + + macros.xml + + + pepcoil -sequence '$input1' -outfile '$out_file1' -window $window -coil $coil -frame $frame -other $other -auto + + + + + + + + + + + + + + + + + + @@ -37,18 +33,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepcoil.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepcoil.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pepinfo.xml --- a/emboss_pepinfo.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepinfo.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,36 +1,27 @@ - + - Plots simple amino acid properties in parallel - emboss - emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto - - - - - - - - - - - - - - - - - + Plots simple amino acid properties in parallel + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepinfo -sequence '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -hwindow $hwindow $plot_type -auto + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepinfo.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepinfo.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pepnet.xml --- a/emboss_pepnet.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepnet.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,41 +1,28 @@ - + - Displays proteins as a helical net - emboss - pepnet -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic $amphipathic -auto - - - - - - - - - - - - - - - - - - - - - - + Displays proteins as a helical net + + macros.xml + + + pepnet -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic $amphipathic -auto + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepnet.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepnet.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pepstats.xml --- a/emboss_pepstats.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepstats.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,19 +1,19 @@ - - Protein statistics - emboss - pepstats -sequence $input1 -outfile $out_file1 -termini $termini -auto - - - - - - - - - - - - + + Protein statistics + + macros.xml + + + pepstats -sequence '$input1' -outfile '$out_file1' -termini $termini -auto + + + + + + + + + @@ -21,18 +21,11 @@ - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepstats.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepstats.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pepwheel.xml --- a/emboss_pepwheel.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepwheel.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,53 +1,35 @@ - + - Shows protein sequences as helices - emboss - emboss_single_outputfile_wrapper.pl pepwheel -sequence $input1 -graph png -goutfile $out_file1 -squares $squares -diamonds $diamonds -octags $octags -amphipathic - $amphipathic -steps $steps -turns $turns -wheel $wheel -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Shows protein sequences as helices + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepwheel -sequence '$input1' -graph png -goutfile '$out_file1' -squares '$squares' -diamonds '$diamonds' -octags '$octags' -amphipathic + $amphipathic -steps $steps -turns $turns -wheel $wheel -auto + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwheel.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepwheel.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pepwindow.xml --- a/emboss_pepwindow.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepwindow.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,30 +1,22 @@ - + - Displays protein hydropathy - emboss - emboss_single_outputfile_wrapper.pl pepwindow -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto - - - - - - - - - - - + Displays protein hydropathy + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepwindow -sequence '$input1' -graph png -goutfile '$out_file1' -length $length -auto + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwindow.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepwindow.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_pepwindowall.xml --- a/emboss_pepwindowall.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_pepwindowall.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,30 +1,22 @@ - + - Displays protein hydropathy of a set of sequences - emboss - emboss_single_outputfile_wrapper.pl pepwindowall -sequence $input1 -graph png -goutfile $out_file1 -length $length -auto - - - - - - - - - - - + Displays protein hydropathy of a set of sequences + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepwindowall -sequence '$input1' -graph png -goutfile '$out_file1' -length $length -auto + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepwindowall.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepwindowall.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_plotcon.xml --- a/emboss_plotcon.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_plotcon.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,30 +1,22 @@ - + - Plot quality of conservation of a sequence alignment - emboss - emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto - - - - - - - - - - - + Plot quality of conservation of a sequence alignment + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' plotcon -sequences '$input1' -graph png -goutfile '$out_file1' -winsize $winsize -auto + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotcon.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/plotcon.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_plotorf.xml --- a/emboss_plotorf.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_plotorf.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,21 +1,18 @@ - + - Plot potential open reading frames - emboss - emboss_single_outputfile_wrapper.pl plotorf -sequence $input1 -graph png -goutfile $out_file1 -start $start -stop $stop -auto - - - - - - - - - - - - - + Plot potential open reading frames + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' plotorf -sequence '$input1' -graph png -goutfile '$out_file1' -start '$start' -stop '$stop' -auto + + + + + + + + --> - .. class:: warningmark The input dataset needs to be sequences. @@ -34,15 +30,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotorf.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/plotorf.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_polydot.xml --- a/emboss_polydot.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_polydot.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,28 +1,24 @@ - + - Displays all-against-all dotplots of a set of sequences - emboss - emboss_single_outputfile_wrapper.pl polydot -sequence $input1 -graph png -goutfile $output2 -outfeat $output1 -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap - $gap -auto - - - - - - - - - - - - - - - - - - - + Displays all-against-all dotplots of a set of sequences + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' polydot -sequence '$input1' -graph png -goutfile '$output2' -outfeat '$output1' -wordsize $wordsize -boxit $boxit -dumpfeat yes -gap + $gap -auto + + + + + + + + + + + + + --> - .. class:: warningmark The input dataset needs to be sequences. @@ -42,15 +37,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/polydot.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/polydot.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_preg.xml --- a/emboss_preg.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_preg.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,29 +1,21 @@ - - Regular expression search of a protein sequence - emboss - preg -sequence $input1 -outfile $out_file1 -pattern "$pattern" -auto - - - - - - - - - - - + + Regular expression search of a protein sequence + + macros.xml + + + preg -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -auto + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/preg.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/preg.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_prettyplot.xml --- a/emboss_prettyplot.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_prettyplot.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,121 +1,83 @@ - + - Displays aligned sequences, with colouring and boxing - emboss - prettyplot -sequences $input1 -graph png -goutfile $out_file1 -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity $cidentity -csimilarity $csimilarity - -cother $cother -docolour $docolour -gtitle $title -pair $pair -identity $identity -box $box -boxcol $boxcol -boxcolval $boxcolval -name $name -maxnamelen $maxnamelen -number $number -listoptions - $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Displays aligned sequences, with colouring and boxing + + macros.xml + + + prettyplot -sequences '$input1' -graph png -goutfile '$out_file1' -residuesperline $residuesperline -resbreak $resbreak -ccolours $ccolours -cidentity '$cidentity' -csimilarity '$csimilarity' + -cother '$cother' -docolour $docolour -gtitle $title -pair '$pair' -identity $identity -box $box -boxcol $boxcol -boxcolval '$boxcolval' -name $name -maxnamelen $maxnamelen -number $number -listoptions + $listoptions -consensus $consensus -collision $collision -alternative $alternative -showscore $showscore -portrait $portrait -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyplot.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/prettyplot.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_prettyseq.xml --- a/emboss_prettyseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_prettyseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,32 +1,28 @@ - - Output sequence with translated ranges - emboss - prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto - - - - - - - - - - - - - - - - - - - - - - - - - + + Output sequence with translated ranges + + macros.xml + + + prettyseq -sequence '$input1' -outfile '$out_file1' -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto + + + + + + + + + + + + + + + + + + @@ -37,9 +33,8 @@ - + - .. class:: warningmark The input dataset needs to be sequences. @@ -47,15 +42,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/prettyseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/prettyseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_primersearch.xml --- a/emboss_primersearch.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_primersearch.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,20 +1,17 @@ - - Searches DNA sequences for matches with primer pairs - emboss - primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto - - - - - - - - - - - - - + + Searches DNA sequences for matches with primer pairs + + macros.xml + + + primersearch -seqall '$input1' -infile '$input2' -outfile '$out_file1' -mismatchpercent $mismatchpercent -auto + + + + + + + @@ -23,19 +20,11 @@ - + - You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/primersearch.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_revseq.xml --- a/emboss_revseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_revseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,56 +1,55 @@ - - Reverse and complement a sequence - emboss - revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Reverse and complement a sequence + + macros.xml + + + + revseq -sequence '$input1' -outseq '$out_file1' -reverse $reverse -complement $complement -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -60,10 +59,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -71,15 +68,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/revseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/revseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_seqmatchall.xml --- a/emboss_seqmatchall.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_seqmatchall.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,34 +1,33 @@ - - All-against-all comparison of a set of sequences - emboss - seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - + + All-against-all comparison of a set of sequences + + macros.xml + + + + seqmatchall -sequence '$input1' -outfile '$out_file1' -wordsize $wordsize -aformat2 $out_format1 -auto + + + + + + + + + + + + + + + + - - - - - . + + + + + @@ -37,10 +36,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -48,15 +45,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqmatchall.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/seqmatchall.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_seqret.xml --- a/emboss_seqret.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_seqret.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,56 +1,55 @@ - - Reads and writes sequences - emboss - seqret -sequence $input1 -outseq $out_file1 -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Reads and writes sequences + + macros.xml + + + + seqret -sequence '$input1' -outseq '$out_file1' -feature $feature -firstonly $firstonly -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -60,19 +59,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/seqret.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/seqret.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_showfeat.xml --- a/emboss_showfeat.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_showfeat.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,131 +1,97 @@ - + - Show features of a sequence - emboss - showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id - $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type - $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Show features of a sequence + + macros.xml + + + + showfeat -sequence '$input1' -outfile '$out_file1' -matchsource '$matchsource' -matchtype '$matchtype' -matchtag '$matchtag' -matchvalue '$matchvalue' -sort $sort -annotation '$annotation' -id + $id -description $description -scale $scale -width $width -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type + $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/showfeat.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_shuffleseq.xml --- a/emboss_shuffleseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_shuffleseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,54 +1,51 @@ - + - Shuffles a set of sequences maintaining composition - emboss - shuffleseq -sequence $input1 -outseq $out_file1 -shuffle "$shuffle" -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Shuffles a set of sequences maintaining composition + + macros.xml + + + + shuffleseq -sequence '$input1' -outseq '$out_file1' -shuffle $shuffle -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - .. class:: warningmark The input dataset needs to be sequences. @@ -56,15 +53,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/shuffleseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/shuffleseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_sigcleave.xml --- a/emboss_sigcleave.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_sigcleave.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,41 +1,39 @@ - - Reports protein signal cleavage sites - emboss - sigcleave -sequence $input1 -outfile $out_file1 -minweight "$minweight" -prokaryote $prokaryote -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Reports protein signal cleavage sites + + macros.xml + + + + sigcleave -sequence '$input1' -outfile '$out_file1' -minweight $minweight -prokaryote $prokaryote -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -45,19 +43,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sigcleave.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sigcleave.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_sirna.xml --- a/emboss_sirna.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_sirna.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,92 +1,87 @@ - - Finds siRNA duplexes in mRNA - emboss - sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2 - -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds siRNA duplexes in mRNA + + macros.xml + + + + sirna -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2 + -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -101,10 +96,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -112,15 +105,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sirna.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_sixpack.xml --- a/emboss_sixpack.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_sixpack.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,128 +1,108 @@ - + - Display a DNA sequence with 6-frame translation and ORFs - emboss - sixpack -sequence $input1 -outfile $ofile1 -outseq $ofile2 -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase - "$uppercase" -number $number -width "$width" -length "$length" -margin "$margin" -name $disp_name -description $description -offset "$offset" -html $html_out1 -osformat $out_format2 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Display a DNA sequence with 6-frame translation and ORFs + + macros.xml + + + + sixpack -sequence '$input1' -outfile '$ofile1' -outseq '$ofile2' -table $table -firstorf $firstorf -lastorf $lastorf -mstart $mstart -reverse $reverse -orfminsize $orfminsize -uppercase + '$uppercase' -number $number -width $width -length $length -margin $margin -name $disp_name -description $description -offset $offset -html $html_out1 -osformat $out_format2 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + --> - .. class:: warningmark The input dataset needs to be sequences. @@ -156,15 +134,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sixpack.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/sixpack.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_skipseq.xml --- a/emboss_skipseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_skipseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,67 +1,57 @@ - - Reads and writes sequences, skipping first few - emboss - skipseq -sequence $input1 -outseq $out_file1 -skip "$skip" -feature $feature -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Reads and writes sequences, skipping first few + + macros.xml + + + + skipseq -sequence '$input1' -outseq '$out_file1' -skip $skip -feature $feature -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/skipseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/skipseq.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_splitter.xml --- a/emboss_splitter.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_splitter.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,57 +1,53 @@ - - Split a sequence into (overlapping) smaller sequences - emboss - splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Split a sequence into (overlapping) smaller sequences + + macros.xml + + + + splitter -sequence '$input1' -outseq '$out_file1' -size $size -overlap $overlap -addoverlap $addoverlap -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -62,10 +58,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -73,15 +67,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/splitter.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/splitter.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_supermatcher.xml --- a/emboss_supermatcher.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_supermatcher.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,47 +1,38 @@ - + - Match large sequences against one or more other sequences - emboss - supermatcher -asequence $input1 -bsequence $input2 -gapopen "$gapopen" -gapextend "$gapextend" -width "$width" -wordlen "$wordlen" -outfile $ofile1 -errorfile $ofile2 -aformat3 - $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Match large sequences against one or more other sequences + + macros.xml + + + + supermatcher -asequence '$input1' -bsequence '$input2' -gapopen $gapopen -gapextend $gapextend -width $width -wordlen $wordlen -outfile '$ofile1' -errorfile '$ofile2' -aformat3 + $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + - + --> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/supermatcher.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/supermatcher.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_syco.xml --- a/emboss_syco.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_syco.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,182 +1,177 @@ - + - Synonymous codon usage Gribskov statistic plot - emboss - emboss_single_outputfile_wrapper.pl syco -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -cfile $cfile -window "$window" -uncommon $uncommon -minimum "$minimum" - -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + Synonymous codon usage Gribskov statistic plot + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' syco -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -cfile $cfile -window $window -uncommon $uncommon -minimum $minimum + -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + --> - You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/syco.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/syco.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_tcode.xml --- a/emboss_tcode.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_tcode.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,52 +1,41 @@ - - Fickett TESTCODE statistic to identify protein-coding DNA - emboss - tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Fickett TESTCODE statistic to identify protein-coding DNA + + macros.xml + + + + tcode -sequence '$input1' -outfile '$out_file1' -window $window -step $step -rformat $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tcode.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tcode.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_textsearch.xml --- a/emboss_textsearch.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_textsearch.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,66 +1,51 @@ - - Search sequence documentation. Slow, use SRS and Entrez! - emboss - textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html - $html_out1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Search sequence documentation. Slow, use SRS and Entrez! + + macros.xml + + + + textsearch -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html + $html_out1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/textsearch.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_tmap.xml --- a/emboss_tmap.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_tmap.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,47 +1,40 @@ - - Displays membrane spanning regions - emboss - emboss_single_outputfile_wrapper.pl tmap -sequences $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -rformat $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Displays membrane spanning regions + + macros.xml + + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' tmap -sequences '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -rformat $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tmap.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tmap.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_tranalign.xml --- a/emboss_tranalign.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_tranalign.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,70 +1,68 @@ - - Align nucleic coding regions given the aligned proteins - emboss - tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Align nucleic coding regions given the aligned proteins + + macros.xml + + + + tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table $table -osformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -74,19 +72,11 @@ - - + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_transeq.xml --- a/emboss_transeq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_transeq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,145 +1,130 @@ - - Translate nucleic acid sequences - emboss - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. 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/transeq.html - ------- - -**Citation** - -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ - - + + Translate nucleic acid sequences + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +The input dataset needs to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html + + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_trimest.xml --- a/emboss_trimest.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_trimest.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,68 +1,62 @@ - - Trim poly-A tails off EST sequences - emboss - trimest -sequence $input1 -outseq $out_file1 -minlength "$minlength" -mismatches "$mismatches" -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1 - -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Trim poly-A tails off EST sequences + + macros.xml + + + + trimest -sequence '$input1' -outseq '$out_file1' -minlength $minlength -mismatches $mismatches -reverse $reverse -tolower $tolower -fiveprime $fiveprime -osformat2 $out_format1 + -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -75,10 +69,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -86,15 +78,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimest.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimest.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_trimseq.xml --- a/emboss_trimseq.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_trimseq.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,72 +1,65 @@ - - Trim ambiguous bits off the ends of sequences - emboss - trimseq -sequence $input1 -outseq $out_file1 -window "$window" -percent "$percent" -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Trim ambiguous bits off the ends of sequences + + macros.xml + + + + trimseq -sequence '$input1' -outseq '$out_file1' -window $window -percent $percent -strict $strict -star $star -left $left -right $right -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -80,10 +73,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -91,15 +82,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/trimseq.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/trimseq.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_twofeat.xml --- a/emboss_twofeat.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_twofeat.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,138 +1,94 @@ - - Finds neighbouring pairs of features in sequences - emboss - twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore" - -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap - -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds neighbouring pairs of features in sequences + + macros.xml + + + + twofeat -sequence '$input1' -outfile '$out_file1' -atype '$atype' -btype '$btype' -minrange $minrange -maxrange $maxrange -asource '$asource' -asense $asense -aminscore $aminscore + -amaxscore $amaxscore -atag '$atag' -avalue '$avalue' -bsource '$bsource' -bsense $bsense -bminscore $bminscore -bmaxscore $bmaxscore -btag '$btag' -bvalue '$bvalue' -overlap $overlap + -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout '$typeout' -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/twofeat.html - \ No newline at end of file + + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_union.xml --- a/emboss_union.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_union.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,46 +1,47 @@ - - Reads sequence fragments and builds one sequence - emboss - union -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Reads sequence fragments and builds one sequence + + macros.xml + + + + union -sequence '$input1' -outseq '$out_file1' -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -48,10 +49,8 @@ - - + - .. class:: warningmark The input dataset needs to be sequences. @@ -59,15 +58,8 @@ ----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/union.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/union.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_vectorstrip.xml --- a/emboss_vectorstrip.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_vectorstrip.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,65 +1,57 @@ - - Strips out DNA between a pair of vector sequences - emboss - vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb - "$linkerb" -osformat4 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Strips out DNA between a pair of vector sequences + + macros.xml + + + + vectorstrip -sequence '$input1' -vectorsfile '$input2' -outseq '$ofile1' -outfile '$ofile2' -vectorfile yes -mismatch $mismatch -besthits $besthits -linkera '$linkera' -linkerb + '$linkerb' -osformat4 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + --> You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/vectorstrip.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_water.xml --- a/emboss_water.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_water.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,43 +1,37 @@ - - Smith-Waterman local alignment - emboss - water -asequence $input1 -bsequence $input2 -outfile $out_file1 -gapopen "$gapopen" -gapextend "$gapextend" -brief $brief -aformat3 $out_format1 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Smith-Waterman local alignment + + macros.xml + + + + water -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -gapopen $gapopen -gapextend $gapextend -brief $brief -aformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -49,26 +43,17 @@ - - + +.. class:: warningmark -.. class:: warningmark +The input datasets need to be sequences. -The input datasets need to be sequences. - ------ +----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/water.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/water.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_wobble.xml --- a/emboss_wobble.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_wobble.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,21 +1,18 @@ - - Wobble base plot - emboss - emboss_single_outputfile_wrapper.pl wobble -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -window "$window" -bases "$bases" -auto - - - - - - - - - - - - - - + + Wobble base plot + + macros.xml + + + perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' wobble -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -window $window -bases '$bases' -auto + + + + + + + + @@ -24,25 +21,17 @@ - + +.. class:: warningmark -.. class:: warningmark +The input dataset needs to be sequences. -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/wobble.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wobble.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_wordcount.xml --- a/emboss_wordcount.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_wordcount.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,17 +1,16 @@ - - Counts words of a specified size in a DNA sequence - emboss - wordcount -sequence $input1 -outfile $out_file1 -wordsize "$wordsize" -auto - - - - - - - - - - + + Counts words of a specified size in a DNA sequence + + macros.xml + + + wordcount -sequence '$input1' -outfile '$out_file1' -wordsize $wordsize -auto + + + + + + @@ -19,25 +18,17 @@ - + +.. class:: warningmark -.. class:: warningmark +The input dataset needs to be sequences. -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/wordcount.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wordcount.html + diff -r 9b98d3d903c6 -r 0e2484b6829b emboss_wordmatch.xml --- a/emboss_wordmatch.xml Fri Aug 12 19:17:10 2016 -0400 +++ b/emboss_wordmatch.xml Mon Jan 30 13:27:40 2017 -0500 @@ -1,51 +1,46 @@ - - Finds all exact matches of a given size between 2 sequences - emboss - wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2 - -offormat5 $out_format3 -auto - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + Finds all exact matches of a given size between 2 sequences + + macros.xml + + + + wordmatch -asequence '$input1' -bsequence '$input2' -outfile '$out_file1' -aoutfeat '$out_file2' -boutfeat '$out_file3' -wordsize $wordsize -aformat3 $out_format1 -offormat4 $out_format2 + -offormat5 $out_format3 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + test takes a long time to run--> +.. class:: warningmark -.. class:: warningmark +The input datasets need to be sequences. -The input datasets need to be sequences. - ------ +----- You can view the original documentation here_. - - .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html - ------- - -**Citation** -For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ - -If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ + .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wordmatch.html - + + diff -r 9b98d3d903c6 -r 0e2484b6829b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 30 13:27:40 2017 -0500 @@ -0,0 +1,14 @@ + + + + emboss + + + + + 10.1016/S0168-9525(00)02024-2 + 10.1101/gr.5578007 + + + +