| Previous changeset 1:b482293b2987 (2015-08-05) Next changeset 3:59252ca85c74 (2016-06-15) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 9fcf62e1e259381613e48a0ff28c27bd4fe82707 |
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modified:
sortmerna.xml tool_dependencies.xml |
| b |
| diff -r b482293b2987 -r 3699b6b771e0 sortmerna.xml --- a/sortmerna.xml Wed Aug 05 02:50:43 2015 -0400 +++ b/sortmerna.xml Tue Mar 29 07:01:13 2016 -0400 |
| [ |
| b'@@ -1,7 +1,7 @@\n-<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.0.0">\n+<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.0">\n <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>\n <requirements>\n- <requirement type=\'package\' version="2.0">sortmerna</requirement>\n+ <requirement type="package" version="2.1b">sortmerna</requirement>\n </requirements>\n <stdio>\n <regex match="This program builds a Burst trie on an input rRNA database"\n@@ -12,6 +12,10 @@\n source="both"\n level="fatal"\n description="The database ${databases} has not been preprocessed using buildtrie before using SortMeRNA." />\n+ <regex match="ERROR"\n+ source="both"\n+ level="fatal"\n+ description="ERROR" />\n </stdio>\n <version_command>\n <![CDATA[\n@@ -22,13 +26,18 @@\n <![CDATA[\n #set $ref = \'\'\n #set $sep=\'\'\n- #if str( $databases_type.databases_selector ) == \'history\':\n+ #if str( $databases_type.databases_selector ) == \'history\'\n #for $db in $databases_type.database_name\n #set $ref += $sep + str($db) + \',\' + $os.path.splitext($os.path.basename(str($db)))[0]\n #set $sep = \':\'\n #end for\n- indexdb_rna --ref $ref\n- &&\n+ #else if str( $databases_type.databases_selector ) == \'cached_to_index\'\n+ ## databases path is not directly accessible, must match by hand with LOC file contents\n+ #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])\n+ #for $db in $databases_type.input_databases.value\n+ #set $ref += $sep + $data_table[$db] + \',\' + $os.path.splitext($data_table[$db])[0] + \'-reindexed\'\n+ #set $sep = \':\'\n+ #end for\n #else:\n ## databases path is not directly accessible, must match by hand with LOC file contents\n #set $data_table = dict([(_[0], _[2]) for _ in $databases_type.input_databases.input.options.tool_data_table.data])\n@@ -37,24 +46,62 @@\n #set $sep = \':\'\n #end for\n #end if\n- sortmerna --ref $ref --reads $input_reads --aligned aligned\n- #if str( $sequencing_type.sequencing_type_selector ) == \'paired\'\n- $sequencing_type.paired_type\n+\n+ #if str( $databases_type.databases_selector ) != \'cached\':\n+ indexdb_rna \n+ --ref $ref \n+ -L $databases_type.seed_length \n+ --max_pos $databases_type.max_pos \n+ &&\n #end if\n- $strand_search\n- $aligned_fastx.aligned_fastx_selector\n- #if $aligned_fastx.aligned_fastx_selector == \'--fastx\'\n- #if $aligned_fastx.other\n- --other other_file\n+\n+ sortmerna \n+ \t--ref $ref \n+ \t--reads $input_reads \n+ \t--aligned aligned\n+\t\n+ \t#if str( $sequencing_type.sequencing_type_selector ) == \'paired\'\n+ \t$sequencing_type.paired_type\n+ \t#end if\n+\n+ \t$strand_search\n+ \t$aligned_fastx.aligned_fastx_selector\n+ \t#if $aligned_fastx.aligned_fastx_selector == \'--fastx\'\n+ \t#if $aligned_fastx.other\n+ \t\t--other other_file\n+ \t#end if\n+ \t#end if\n+ \t$aligned_sam.aligned_sam_selector\n+ \t#if $aligned_sam.aligned_sam_selector == \'--sam\'\n+ \t$aligned_sam.sq\n+ \t#end if\n+ \t$aligned_blast\n+\n+ \t$log\n+\n+ #if $report.report_type == \'best\'\n+ #if $report.report_best.report_best_type == \'1\'\n+ --best 1\n+ --min_lis $report.report_best.report_best_min_lis\n+ #else\n+ --best $report.report_best.report_best_value\n+ --min_lis $report.report_best.report_best_min_lis\n+ #end if\n+ #else\n+ #if $report.report_num_alignments.report_num_alignments_type == \'other_value\'\n+ --num_alignments $report.report_num_alignments.report_num_alignments_value\n+ #else\n+ -'..b' using a LIS of seed matches)</option>\n+ <option value="other_value">A custom number of reference sequences are searched for alignments (speed decrease for high value)</option>\n+ </param>\n+ <when value="1">\n+ <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds\' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>\n+ </when>\n+ <when value="other_value">\n+ <param name="report_best_value" type="integer" min="2" max="100" value="2" label="Number of alignments to be made" help="Only the best one is reported. The computation speed decrease with high value"/>\n+ <param name="report_best_min_lis" type="integer" min="0" max="100" value="2" label="Number of longest LIS an alignement needs to be searched" help="The alignements having the first INT longest LIS. LIS stands for Longest Increasing Subsequence, it is computed using seeds\' positions to expand hits into longer matches prior to Smith-Waterman alignment. (--min_lis)"/>\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="num_alignments">\n+ <conditional name="report_num_alignments">\n+ <param name="report_num_alignments_type" type="select" label="Number of output alignments" help="(--num_alignments)">\n+ <option value="0">All alignments reaching the E-value threshold are reported (very slow, this option is not suggested for high similarity rRNA databases)</option>\n+ <option value="1" selected="true">The first alignment passing E-value threshold are reported (very fast, best choice if only filtering is needed)</option>\n+ <option value="other_value">A custom number of alignments are made and reported (speed decrease for high value)</option>\n+ </param>\n+ <when value="0" />\n+ <when value="1" />\n+ <when value="other_value">\n+ <param name="report_num_alignments_value" type="integer" min="0" max="100" value="1" label="Number of alignments to be made and reported" help=""/>\n+ </when>\n+ </conditional>\n+ </when>\n+ </conditional>\n+\n+ <param name="e_value" type="float" min="0" max="10" value="1" label="E-value threshold" help="(-e)"/>\n+ <param name="match" type="integer" min="0" max="10" value="2" label="SW score for a match" help="(--match)"/>\n+ <param name="mismatch" type="integer" min="-10" max="0" value="-3" label="SW penalty for a mismatch" help="(--mismatch)"/>\n+ <param name="gap_open" type="integer" min="0" max="10" value="5" label="SW penalty for introducing a gap" help="(--gap_open)"/>\n+ <param name="gap_ext" type="integer" min="0" max="10" value="2" label="SW penalty for extending a gap" help="(--gap_ext)"/>\n+ <param name="ambiguous_letter" type="integer" min="-10" max="0" value="-3" label="SW penalty for ambiguous letters (N\'s)" help="(-N)"/>\n </inputs>\n <outputs>\n <data format_source="input_reads" name="output_fastx" from_work_dir="aligned.dat"\n@@ -245,8 +346,10 @@\n \n .. class:: warningmark\n \n-Note that your personal databases are indexed each time, and that\n-this may take some time depending on the size of the given database.\n+Note that your personal databases are indexed each time. The public ribosomal\n+databases are indexed when added, but they can be re-indexed with non-default indexing \n+parameters. The indexing may take some time depending on the size of the given database.\n+\n ]]>\n </help>\n \n' |
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| diff -r b482293b2987 -r 3699b6b771e0 tool_dependencies.xml --- a/tool_dependencies.xml Wed Aug 05 02:50:43 2015 -0400 +++ b/tool_dependencies.xml Tue Mar 29 07:01:13 2016 -0400 |
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| @@ -1,18 +1,49 @@ <?xml version="1.0"?> <tool_dependency> - <package name="sortmerna" version="2.0"> + <package name="sortmerna" version="2.1b"> <install version="1.0"> - <actions> - <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action> - <action type="autoconf"/> - <action type="set_environment"> - <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> + <actions_group> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url" target_filename="sortmerna-2.1b.tar.gz">https://github.com/biocore/sortmerna/archive/2.1b.tar.gz</action> + <action type="shell_command"><![CDATA[ + ./build.sh --prefix=$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++ 4.3 or later. Installation may take a moment since ribosomal databases have to be indexed. + 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> |