# HG changeset patch # User iracooke # Date 1445387690 14400 # Node ID 68d8c9e521d7017f09d963b85d55e87939300b9a # Parent a85c8de9630a3bcd8311cd6b13ac88794de6daac planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty diff -r a85c8de9630a -r 68d8c9e521d7 gff3_to_fasta.xml --- a/gff3_to_fasta.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/gff3_to_fasta.xml Tue Oct 20 20:34:50 2015 -0400 @@ -1,40 +1,29 @@ - - - iracooke/protk-1.4.1 - protk + + Extract proteins from gff3 and encode genomic coordinates in the fasta header + + iracooke/protk-1.4.3 + protk - - Extract proteins from gff3 and encode genomic coordinates in the fasta header - - - augustus_to_proteindb.rb $gff_file -o $output $coords - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + augustus_to_proteindb.rb $gff_file -o $output $coords + + + + + + + + + + + + + + + **What it does** @@ -42,11 +31,5 @@ Extract proteins from gff3 and encode genomic coordinates in the fasta header. Currently this only works with gff3 generated using the Augustus gene finder ----- - -**References** - - - diff -r a85c8de9630a -r 68d8c9e521d7 mzid_to_protxml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzid_to_protxml.xml Tue Oct 20 20:34:50 2015 -0400 @@ -0,0 +1,53 @@ + + Convert mzIdentML to protXML + + + iracooke/protk-1.4.3 + protk + blast+ + + + + mzid_to_protxml.rb $mzid_file + + -o $output + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Roughly converts mzIdentML to protXML. + +At the present time, the conversion is really only designed to work with mzIdentML files produced by PeptideShaker and to produce protXML files suitable for input to protk proteogenomics tools. + + + + + diff -r a85c8de9630a -r 68d8c9e521d7 protxml_to_gff.xml --- a/protxml_to_gff.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/protxml_to_gff.xml Tue Oct 20 20:34:50 2015 -0400 @@ -1,102 +1,120 @@ - Export Proteomics Data to GFF + Export Proteomics Data to GFF + + iracooke/protk-1.4.3 + protk + blast+ + + + + + + protxml_to_gff.rb $protxml_file + #if $database.source_select=="built_in": + -d $database.dbkey + #else + -d $database.fasta_file + #end if + -c $gene_file + #if str( $gffidpattern ): + --gff-idregex='$gffidpattern' + #end if - - iracooke/protk-1.4.1 - protk - blast+ - + #if str( $genomeidpattern ): + --genome-idregex='$genomeidpattern' + #end if - - protxml_to_gff.rb $protxml_file - - #if $database.source_select=="built_in": - -d $database.dbkey - #else - -d $database.fasta_file - #end if + #if str( $ignorepattern ): + --ignore-regex='$ignorepattern' + #end if + + --threshold=$peptide_threshold + --prot-threshold=$prot_threshold + $stack_charges + -o $output + + + + + + + + + + Database + + + + + + + + + + + + + + + + + + + + + + + + + - -c $gene_file + + + + + + + + + + - --gff-idregex='$gffidpattern' - - -o $output + + + + + + + + + + - - - - - - - - - - - - - - Database - - - - - - - - - - - - - - + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + **What it does** Exports peptides and proteins to gff ----- - -**References** - - - - + diff -r a85c8de9630a -r 68d8c9e521d7 repository_dependencies.xml --- a/repository_dependencies.xml Thu Mar 26 20:16:00 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r a85c8de9630a -r 68d8c9e521d7 test-data/PeptideShaker_tiny.mzid --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PeptideShaker_tiny.mzid Tue Oct 20 20:34:50 2015 -0400 @@ -0,0 +1,1725 @@ + + + + + + + + + + + + + + + + + + + No customisations + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + KSPVYKVHFTR + + + SQIPFLVLFDPIEAAR + + + SSGNWLNLFNPATPSFR + + + GGIDSWNALGYIPVQDFDYK + + + GQSGNPMLMLDLTDLSDSR + + + TLEYSYNDFCISEMAAGLGGR + + + + + + TALFNFRFPK + + + NWIGHEFFLK + + + TWGFQDPLGCSQIDEK + + + + + + DGHVFAGASLPYGLAK + + + SLIDTYKHEGWLPDCR + + + + + + DATVEPFDWCCQGR + + + + + + + + + LVNNIAVEMTTAR + + + IYDTGIFANSR + + + SINGYPLPGGGTVR + + + FEPPAKETDPITAR + + + ENIDWNEGYK + + + RAHYYVPR + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r a85c8de9630a -r 68d8c9e521d7 tool_dependencies.xml --- a/tool_dependencies.xml Thu Mar 26 20:16:00 2015 -0400 +++ b/tool_dependencies.xml Tue Oct 20 20:34:50 2015 -0400 @@ -1,8 +1,9 @@ - + + + - + -