# HG changeset patch # User p.lucas # Date 1718024504 0 # Node ID eda2d4904bdd28a222aa54343359b67f781b1204 # Parent 08f50579102b035ee7716f414ff1f64bd344e7d5 Uploaded diff -r 08f50579102b -r eda2d4904bdd diamond.xml --- a/diamond.xml Thu Jun 06 13:46:22 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,378 +0,0 @@ - - alignment tool for short sequences against a protein database - - macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - [0-9,]* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - -
-
- - - - - - -
-
- - - - output_section['output_unal'] and "--un" in output_section['output_unal'] - - - output_section['output_unal'] and "--un" in output_section['output_unal'] - - - - - - -
diff -r 08f50579102b -r eda2d4904bdd diamond_makedb.xml --- a/diamond_makedb.xml Thu Jun 06 13:46:22 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ - - Build database from a FASTA file - - macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 08f50579102b -r eda2d4904bdd diamond_view.xml --- a/diamond_view.xml Thu Jun 06 13:46:22 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,66 +0,0 @@ - - generate formatted output from DAA files - - macros.xml - - - - - - - -
- -
- - -
- - - - - - - -
diff -r 08f50579102b -r eda2d4904bdd macros.xml --- a/macros.xml Thu Jun 06 13:46:22 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,173 +0,0 @@ - - 2.1.9 - 0 - - - - - - - - - /usr/bin/diamond version | cut -d" " -f 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 10.1038/nmeth.3176 - - - - - - - output_section["output"]["outfmt"] == "0" - - - output_section["output"]["outfmt"] == "5" - - - output_section["output"]["outfmt"] == "6" - - - - output_section["output"]["outfmt"] == "100" - - - output_section["output"]["outfmt"] == "101" - - - output_section["output"]["outfmt"] == "102" - - - - - #if $output_section.output.outfmt == "0" - --outfmt '0' - --out '$blast_pairw' - #else if $output_section.output.outfmt == "5" - --outfmt '5' - --out '$blast_xml' - #else if $output_section.output.outfmt == "6" - --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(',')) - --out '$blast_tabular' - --unal $output_section.output.unal - #else if $output_section.output.outfmt == "100" - --outfmt '100' - $output_section.output.salltitles - $output_section.output.sallseqid - --out output.daa - #else if $output_section.output.outfmt == "101" - --outfmt '101' - $output_section.output.salltitles - $output_section.output.sallseqid - --out '$sam_output' - #else if $output_section.output.outfmt == "102" - --outfmt '102' - --out '$tax_output' - #end if - - - - #if str($hit_filter.hit_filter_select) == 'max': - --max-target-seqs '$hit_filter.max_target_seqs' - #else: - --top '$hit_filter.top' - #end if - - diff -r 08f50579102b -r eda2d4904bdd tool-data/pl_diamond_database.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/pl_diamond_database.loc Mon Jun 10 13:01:44 2024 +0000 @@ -0,0 +1,11 @@ +#This is a sample file that enables the diamind to find the protein databases +#You will need to create these data files and then create +#a diamond_database.loc file similar to this one (store it in this directory) +#that points to the directories in which those files are stored. +#The diamond_database_indices.loc file has this format (longer white space characters are TAB characters): +# +# +# +#So, for example: +#ncbi_nr NCBI NR database (1-1-2015) /data/db/diamond/1-1-2015/nr.dmnd + diff -r 08f50579102b -r eda2d4904bdd tool-data/pl_diamond_database.loc.sample --- a/tool-data/pl_diamond_database.loc.sample Thu Jun 06 13:46:22 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -#This is a sample file that enables the diamind to find the protein databases -#You will need to create these data files and then create -#a diamond_database.loc file similar to this one (store it in this directory) -#that points to the directories in which those files are stored. -#The diamond_database_indices.loc file has this format (longer white space characters are TAB characters): -# -# -# -#So, for example: -#ncbi_nr NCBI NR database (1-1-2015) /data/db/diamond/1-1-2015/nr.dmnd - -nr_nfs NR_NFS /nfs/data/db/nr_blast/nr diff -r 08f50579102b -r eda2d4904bdd tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Jun 06 13:46:22 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - - - - - value, name, db_path - -
-