Mercurial > repos > rnateam > sortmerna
changeset 5:cd8c76234b0c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 65d322f9ab2f24d65b307f3553589149a1d678d5
| author | rnateam |
|---|---|
| date | Wed, 31 May 2017 14:55:32 -0400 |
| parents | 1bdb57965c6f |
| children | 185effcdfb68 |
| files | macros.xml readme.md sortmerna.xml tool-data/rRNA_databases.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 6 files changed, 17 insertions(+), 86 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed May 31 14:55:32 2017 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0" ?> +<macros> + <token name="@VERSION@">2.1b</token> +</macros> \ No newline at end of file
--- a/readme.md Thu May 11 10:28:11 2017 -0400 +++ b/readme.md Wed May 31 14:55:32 2017 -0400 @@ -15,6 +15,8 @@ .. _`Galaxy Tool Shed`: https://testtoolshed.g2.bx.psu.edu/view/bgruening/sortmerna +To install the databases, we recommend to use the dedicated data manager available in the `Galaxy Tool Shed` + ======= History
--- a/sortmerna.xml Thu May 11 10:28:11 2017 -0400 +++ b/sortmerna.xml Wed May 31 14:55:32 2017 -0400 @@ -1,7 +1,10 @@ -<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.2"> +<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.3"> <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description> + <macros> + <import>macros.xml</import> + </macros> <requirements> - <requirement type="package" version="2.1b">sortmerna</requirement> + <requirement type="package" version="@VERSION@">sortmerna</requirement> </requirements> <stdio> <regex match="This program builds a Burst trie on an input rRNA database" @@ -33,16 +36,16 @@ #end for #else if str( $databases_type.databases_selector ) == 'cached_to_index' ## databases path is not directly accessible, must match by hand with LOC file contents - #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) + #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) #for $db in $databases_type.input_databases.value - #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] + '-reindexed' + #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] + '-reindexed' #set $sep = ':' #end for #else: ## databases path is not directly accessible, must match by hand with LOC file contents - #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) + #set $data_table = dict([(_[0], _[3]) for _ in $databases_type.input_databases.input.options.tool_data_table.data]) #for $db in $databases_type.input_databases.value - #set $ref += $sep + $data_table[$db] + ',' + $os.path.splitext($data_table[$db])[0] + #set $ref += $sep + $data_table[$db] + '.fasta,' + $data_table[$db] #set $sep = ':' #end for #end if
--- a/tool-data/rRNA_databases.loc.sample Thu May 11 10:28:11 2017 -0400 +++ b/tool-data/rRNA_databases.loc.sample Wed May 31 14:55:32 2017 -0400 @@ -1,30 +1,1 @@ -#This is a sample file distributed with Galaxy that is used to define a -#list of public ribosomal databases for SortMeRNA, using the following format -#(white space characters are TAB characters): -# -#<unique_id> <database_caption> <fasta_file_path> -# -#So, for example, if your database is rfam-5.8s-id98 and the path to your FASTA -#file is /data/rRNA_databases/rfam-5.8s-id98.fasta, then the rRNA_databases.loc -#entry would look like this: -# -#rfam-5.8s-id98 Rfam 5.8S eukarya /data/rRNA_databases/rfam-5.8s-id98.fasta -# -#For each rRNA database, you need to create the index files using the -#indexdb_rna program provided by SortMeRNA. You need to specify as index -#basename the path of the FASTA file without extension. For example, for the -#previous database the command is: -# -# indexdb_rna --ref /data/rRNA_databases/rfam-5.8s-id98.fasta,/data/rRNA_databases/rfam-5.8s-id98 -# -#Since SortMeRNA comes bundled with eight ribosomal databases, you can use them -#by creating the actual index files as explained above and uncommenting the -#following lines. -#rfam-5.8s-id98 Rfam 5.8S eukarya $SORTMERNADIR/rRNA_databases/rfam-5.8s-database-id98.fasta -#rfam-5s-id98 Rfam 5S archaea/bacteria $SORTMERNADIR/rRNA_databases/rfam-5s-database-id98.fasta -#silva-arc-16s-id95 SILVA v.119 16S archaea $SORTMERNADIR/rRNA_databases/silva-arc-16s-id95.fasta -#silva-arc-23s-id98 SILVA v.119 23S archaea $SORTMERNADIR/rRNA_databases/silva-arc-23s-id98.fasta -#silva-bac-16s-id90 SILVA v.119 16S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-16s-id90.fasta -#silva-bac-23s-id98 SILVA v.119 23S bacteria $SORTMERNADIR/rRNA_databases/silva-bac-23s-id98.fasta -#silva-euk-18s-id95 SILVA v.119 18S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-18s-id95.fasta -#silva-euk-28s-id98 SILVA v.119 28S eukarya $SORTMERNADIR/rRNA_databases/silva-euk-28s-id98.fasta +#<unique_id> <database_caption> <name> <fasta_file_path>
--- a/tool_data_table_conf.xml.sample Thu May 11 10:28:11 2017 -0400 +++ b/tool_data_table_conf.xml.sample Wed May 31 14:55:32 2017 -0400 @@ -1,7 +1,7 @@ <tables> <!-- Locations of public ribosomal databases --> <table name="rRNA_databases" comment_char="#"> - <columns>value, name, path</columns> + <columns>value, name, dbkey, path</columns> <file path="tool-data/rRNA_databases.loc" /> </table> </tables>
--- a/tool_dependencies.xml Thu May 11 10:28:11 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,49 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="sortmerna" version="2.1b"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action> - <action type="shell_command"><![CDATA[ - ./build.sh --prefix=$INSTALL_DIR - ]]> - </action> - <action type="shell_command">make install</action> - <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action> - <action type="move_directory_files"> - <source_directory>rRNA_databases/</source_directory> - <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - <actions architecture="x86_64" os="darwin"> - <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action> - <action type="shell_command"><![CDATA[ - export CC=gcc-mp-4.8 && export CXX=g++-mp-4.8 && ./build.sh --prefix=$INSTALL_DIR && make install - ]]> - </action> - <action type="make_directory">$INSTALL_DIR/rRNA_databases/</action> - <action type="move_directory_files"> - <source_directory>rRNA_databases/</source_directory> - <destination_directory>$INSTALL_DIR/rRNA_databases/</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </actions_group> - </install> - <readme> - SortMeRNA requires g++ 4.8 or later. - - Note: the Clang compiler on Mac (distributed through Xcode) does not - support multithreading. The user is recommended to install the original - GCC compiler via MacPorts - </readme> - </package> -</tool_dependency>