details: http://www.bx.psu.edu/hg/galaxy/rev/69a04e6bd513 changeset: 3279:69a04e6bd513 user: Greg Von Kuster <greg@bx.psu.edu> date: Wed Jan 27 08:51:23 2010 -0500 description: Update tool_conf.xml.main and the tool conf for eupathdb. diffstat: tool_conf.xml.main | 24 +++++++++++++----------- tools/data_source/eupathdb.xml | 2 +- 2 files changed, 14 insertions(+), 12 deletions(-) diffs (75 lines): diff -r e25fbd7cd958 -r 69a04e6bd513 tool_conf.xml.main --- a/tool_conf.xml.main Tue Jan 26 19:52:38 2010 -0500 +++ b/tool_conf.xml.main Wed Jan 27 08:51:23 2010 -0500 @@ -8,8 +8,6 @@ <tool file="data_source/biomart.xml" /> <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/flymine.xml" /> - <tool file="data_source/modmine.xml" /> - <tool file="data_source/ratmine.xml" /> <tool file="data_source/eupathdb.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> @@ -49,7 +47,6 @@ <tool file="maf/maf_to_fasta.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="filters/wiggle_to_simple.xml" /> </section> <section name="FASTA manipulation" id="fasta_manipulation"> <tool file="fasta_tools/fasta_compute_length.xml" /> @@ -98,7 +95,7 @@ <tool file="extract/phastOdds/phastOdds_tool.xml" /> </section> <section name="Operate on Genomic Intervals" id="bxops"> - <tool file="new_operations/intersect.xml" /> + <tool file="new_operations/intersect.xml" /> <tool file="new_operations/subtract.xml" /> <tool file="new_operations/merge.xml" /> <tool file="new_operations/concat.xml" /> @@ -277,16 +274,20 @@ <tool file="metag_tools/short_reads_figure_score.xml" /> <tool file="metag_tools/short_reads_trim_seq.xml" /> <label text="AB-SOLiD data" id="solid" /> - <tool file="next_gen_conversion/solid_to_fastq.xml" /> + <tool file="next_gen_conversion/solid2fastq.xml" /> <tool file="solid_tools/solid_qual_stats.xml" /> <tool file="solid_tools/solid_qual_boxplot.xml" /> </section> - <section name="NGS: Mapping" id="solexa_tools"> - <tool file="sr_mapping/bowtie_wrapper.xml" /> - <tool file="sr_mapping/bwa_wrapper.xml" /> - <!-- <tool file="sr_mapping/lastz_wrapper.xml" /> --> - <tool file="metag_tools/megablast_wrapper.xml" /> - <tool file="metag_tools/megablast_xml_parser.xml" /> + <section name="NGS: Mapping" id="ngs_mapping"> + <label text="Illumina" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> + <label text="Roche-454" /> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <label text="AB-SOLiD" /> + <tool file="sr_mapping/bowtie_color_wrapper.xml" /> </section> <section name="NGS: SAM Tools" id="samtools"> <tool file="samtools/sam_bitwise_flag_filter.xml" /> @@ -297,4 +298,5 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> + </toolbox> diff -r e25fbd7cd958 -r 69a04e6bd513 tools/data_source/eupathdb.xml --- a/tools/data_source/eupathdb.xml Tue Jan 26 19:52:38 2010 -0500 +++ b/tools/data_source/eupathdb.xml Wed Jan 27 08:51:23 2010 -0500 @@ -6,7 +6,7 @@ <tool name="EuPathDB" id="eupathdb" tool_type="data_source"> <description>server</description> <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> - <inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post"> + <inputs action="http://eupathdb.org/eupathdb/queries_tools.jsp" check_values="false" method="post"> <display>go to EuPathDB server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" /> </inputs>