# HG changeset patch # User p.lucas # Date 1717057441 0 # Node ID a5dd4de5e8076c865b5c536109c090fa6a8529de # Parent d680d59f838a9d0836ea3ac889dbd8126df3f65d Uploaded diff -r d680d59f838a -r a5dd4de5e807 diamond.xml --- a/diamond.xml Thu May 30 07:36:06 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,699 +0,0 @@ - - alignment tool for short sequences against a protein database - - macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - [0-9,]* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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diff -r d680d59f838a -r a5dd4de5e807 diamond_makedb.xml --- a/diamond_makedb.xml Thu May 30 07:36:06 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,90 +0,0 @@ - - Build database from a FASTA file - - macros.xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r d680d59f838a -r a5dd4de5e807 diamond_view.xml --- a/diamond_view.xml Thu May 30 07:36:06 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,106 +0,0 @@ - - generate formatted output from DAA files - - macros.xml - - - - - - - -
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diff -r d680d59f838a -r a5dd4de5e807 macros.xml --- a/macros.xml Thu May 30 07:36:06 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 d680d59f838a -r a5dd4de5e807 tool-data/PL_diamond_database.loc --- a/tool-data/PL_diamond_database.loc Thu May 30 07:36:06 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 d680d59f838a -r a5dd4de5e807 tool-data/PL_diamond_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/PL_diamond_database.loc.sample Thu May 30 08:24:01 2024 +0000 @@ -0,0 +1,12 @@ +#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 d680d59f838a -r a5dd4de5e807 tool_data_table_conf.xml --- a/tool_data_table_conf.xml Thu May 30 07:36:06 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - - - - - value, name, db_path - -
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diff -r d680d59f838a -r a5dd4de5e807 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu May 30 07:36:06 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ - - - - - value, name, db_path - -
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