diff --git a/tools/emboss_5/emboss_primersearch.xml b/tools/emboss_5/emboss_primersearch.xml new file mode 100644 index 00000000000..15857860837 --- /dev/null +++ b/tools/emboss_5/emboss_primersearch.xml @@ -0,0 +1,32 @@ + + Searches DNA sequences for matches with primer pairs + primersearch -seqall $input1 -infile $input2 -outfile $out_file1 -mismatchpercent $mismatchpercent -auto + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/primersearch.html + + diff --git a/tools/emboss_5/emboss_revseq.xml b/tools/emboss_5/emboss_revseq.xml new file mode 100644 index 00000000000..45aeddc78b4 --- /dev/null +++ b/tools/emboss_5/emboss_revseq.xml @@ -0,0 +1,89 @@ + + Reverse and complement a sequence + revseq -sequence $input1 -outseq $out_file1 -reverse $reverse -complement $complement -osformat2 $out_format1 -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/revseq.html + + diff --git a/tools/emboss_5/emboss_seqmatchall.xml b/tools/emboss_5/emboss_seqmatchall.xml new file mode 100644 index 00000000000..df920171a5c --- /dev/null +++ b/tools/emboss_5/emboss_seqmatchall.xml @@ -0,0 +1,53 @@ + + All-against-all comparison of a set of sequences + seqmatchall -sequence $input1 -outfile $out_file1 -wordsize $wordsize -aformat2 $out_format1 -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/seqmatchall.html + + diff --git a/tools/emboss_5/emboss_sirna.xml b/tools/emboss_5/emboss_sirna.xml new file mode 100644 index 00000000000..9da26fd88cb --- /dev/null +++ b/tools/emboss_5/emboss_sirna.xml @@ -0,0 +1,117 @@ + + Finds siRNA duplexes in mRNA + sirna -sequence $input1 -outfile $ofile1 -outseq $ofile2 -poliii $poliii -aa $aa -tt $tt -polybase $polybase -context $context -rformat2 $out_format1 -osformat3 $out_format2 + -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/sirna.html + + diff --git a/tools/emboss_5/emboss_splitter.xml b/tools/emboss_5/emboss_splitter.xml new file mode 100644 index 00000000000..b184f621cea --- /dev/null +++ b/tools/emboss_5/emboss_splitter.xml @@ -0,0 +1,78 @@ + + Split a sequence into (overlapping) smaller sequences + splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -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/splitter.html + + diff --git a/tools/emboss_5/emboss_tranalign.xml b/tools/emboss_5/emboss_tranalign.xml new file mode 100644 index 00000000000..f2019c011a2 --- /dev/null +++ b/tools/emboss_5/emboss_tranalign.xml @@ -0,0 +1,83 @@ + + Align nucleic coding regions given the aligned proteins + tranalign -asequence $input1 -bsequence $input2 -outseq $out_file1 -table $table -osformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tranalign.html + + diff --git a/tools/emboss_5/emboss_transeq.xml b/tools/emboss_5/emboss_transeq.xml new file mode 100644 index 00000000000..dd207d8a4d4 --- /dev/null +++ b/tools/emboss_5/emboss_transeq.xml @@ -0,0 +1,121 @@ + + Translate nucleic acid sequences + transeq -sequence $input1 -outseq $out_file1 -frame $frame -table $table -regions "$regions" -trim $trim -clean $clean -alternative $alternative -osformat2 $out_format1 -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/transeq.html + +