details: http://www.bx.psu.edu/hg/galaxy/rev/46852d01ff16 changeset: 2742:46852d01ff16 user: rc date: Mon Sep 21 15:43:38 2009 -0400 description: Merge with ad4f25a155f02f31edabc5baa822a92610e9b4f4

0 file(s) affected in this change:

diffs (59 lines):

diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/barcode_splitter_output_example.png Binary file static/fastx_icons/barcode_splitter_output_example.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fasta_clipping_histogram_1.png Binary file static/fastx_icons/fasta_clipping_histogram_1.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fasta_clipping_histogram_2.png Binary file static/fastx_icons/fasta_clipping_histogram_2.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastq_nucleotides_distribution_1.png Binary file static/fastx_icons/fastq_nucleotides_distribution_1.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastq_nucleotides_distribution_2.png Binary file static/fastx_icons/fastq_nucleotides_distribution_2.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastq_nucleotides_distribution_3.png Binary file static/fastx_icons/fastq_nucleotides_distribution_3.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastq_nucleotides_distribution_4.png Binary file static/fastx_icons/fastq_nucleotides_distribution_4.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastq_quality_boxplot_1.png Binary file static/fastx_icons/fastq_quality_boxplot_1.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastq_quality_boxplot_2.png Binary file static/fastx_icons/fastq_quality_boxplot_2.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastq_quality_boxplot_3.png Binary file static/fastx_icons/fastq_quality_boxplot_3.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 static/fastx_icons/fastx_clipper_example.png Binary file static/fastx_icons/fastx_clipper_example.png has changed diff -r 2f2c07fa1a39 -r 46852d01ff16 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Sep 21 15:40:58 2009 -0400 +++ b/tool_conf.xml.sample Mon Sep 21 15:43:38 2009 -0400 @@ -170,7 +170,7 @@ <tool file="fastx_toolkit/fastx_collapser.xml" /> </section> <section name="NGS: QC and manipulation" id="cshl_library_information"> - <label text="Genetic FASTQ data" id="fastq" /> + <label text="Generic FASTQ data" id="fastq" /> <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> @@ -185,10 +185,10 @@ <tool file="fastx_toolkit/fastq_quality_filter.xml" /> <!--<tool file="fastx_toolkit/fastx_barcode_splitter.xml" />--> <tool file="metag_tools/split_paired_reads.xml" /> - <label text="Roche-454 Specific" id="454" /> + <label text="Roche-454 data" id="454" /> <tool file="metag_tools/short_reads_figure_score.xml" /> <tool file="metag_tools/short_reads_trim_seq.xml" /> - <label text="AB-SOLiD Specific" id="solid" /> + <label text="AB-SOLiD data" id="solid" /> <tool file="solid_tools/solid_qual_stats.xml" /> <tool file="solid_tools/solid_qual_boxplot.xml" /> </section> diff -r 2f2c07fa1a39 -r 46852d01ff16 tools/samtools/sam2interval.xml --- a/tools/samtools/sam2interval.xml Mon Sep 21 15:40:58 2009 -0400 +++ b/tools/samtools/sam2interval.xml Mon Sep 21 15:43:38 2009 -0400 @@ -55,7 +55,7 @@ ref 28 33 - r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 ref 36 45 - r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *

-Setting *Print all?* is set to **No** will generate the following:: +Setting *Print all?* to **No** will generate the following::

ref 6 22 + r001 ref 8 19 + r002