- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2745: Second pass of help and interface updates. Not...
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e9104d403af7 changeset: 2745:e9104d403af7 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Tue Sep 22 08:59:36 2009 -0400 description: Second pass of help and interface updates. Not done yet... 19 file(s) affected in this change: static/images/solid_qual.png tool_conf.xml.sample tools/fastx_toolkit/fastq_quality_boxplot.xml tools/fastx_toolkit/fastq_quality_converter.xml tools/fastx_toolkit/fastq_quality_filter.xml tools/fastx_toolkit/fastq_to_fasta.xml tools/fastx_toolkit/fastx_artifacts_filter.xml tools/fastx_toolkit/fastx_nucleotides_distribution.xml tools/fastx_toolkit/fastx_quality_statistics.xml tools/fastx_toolkit/fastx_renamer.xml tools/fastx_toolkit/fastx_reverse_complement.xml tools/fastx_toolkit/fastx_trimmer.xml tools/metag_tools/short_reads_figure_score.xml tools/metag_tools/short_reads_trim_seq.xml tools/metag_tools/split_paired_reads.xml tools/solid_tools/solid_qual_boxplot.xml tools/solid_tools/solid_qual_stats.xml tools/sr_mapping/bowtie_wrapper.xml tools/sr_mapping/bwa_wrapper.xml diffs (499 lines): diff -r 97381671a8e7 -r e9104d403af7 static/images/solid_qual.png Binary file static/images/solid_qual.png has changed diff -r 97381671a8e7 -r e9104d403af7 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Sep 21 20:13:20 2009 -0400 +++ b/tool_conf.xml.sample Tue Sep 22 08:59:36 2009 -0400 @@ -70,8 +70,10 @@ <tool file="maf/maf_to_interval.xml" /> <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="next_gen_conversion/solid_to_fastq.xml" /> <tool file="next_gen_conversion/fastq_conversions.xml" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> </section> <section name="Extract Features" id="features"> <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> @@ -175,8 +177,6 @@ <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />  - <tool file="fastx_toolkit/fastq_to_fasta.xml" /> - <tool file="fastx_toolkit/fastq_quality_converter.xml" />  <tool file="fastx_toolkit/fastx_trimmer.xml" /> <tool file="fastx_toolkit/fastx_renamer.xml" /> diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastq_quality_boxplot.xml --- a/tools/fastx_toolkit/fastq_quality_boxplot.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_boxplot.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,10 +1,10 @@ -<tool id="cshl_fastq_quality_boxplot" name="Quality Score"> - <description>chart</description> +<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot"> + <description></description> <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command> <inputs> - <param format="txt" name="input" type="data" label="Statistics report file (output of 'FASTQ Statistics' tool)" /> + <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" /> </inputs> <outputs> @@ -42,6 +42,14 @@ .. image:: ../static/fastx_icons/fastq_quality_boxplot_3.png +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + + + </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastq_quality_converter.xml --- a/tools/fastx_toolkit/fastq_quality_converter.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_converter.xml Tue Sep 22 08:59:36 2009 -0400 @@ -85,7 +85,12 @@ +CSHL__2_FC042AGWWWXX:8:1:103:1185 hhhhhca_hhh`^Vh@IVQNHdObVLWCJ@HBDY^B +------ +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastq_quality_filter.xml --- a/tools/fastx_toolkit/fastq_quality_filter.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastq_quality_filter.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="cshl_fastq_quality_filter" name="Quality Filter"> +<tool id="cshl_fastq_quality_filter" name="Filter by quality"> <description></description> <command>zcat -f '$input' | fastq_quality_filter -q $quality -p $percent -v -o $output</command> @@ -67,7 +67,11 @@ Using **percent = 100** and **cut-off = 20** - This read will be discarded (not all cycles have quality equal to / higher than 20). - +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastq_to_fasta.xml --- a/tools/fastx_toolkit/fastq_to_fasta.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastq_to_fasta.xml Tue Sep 22 08:59:36 2009 -0400 @@ -65,6 +65,11 @@ >1 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastx_artifacts_filter.xml --- a/tools/fastx_toolkit/fastx_artifacts_filter.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastx_artifacts_filter.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,9 +1,9 @@ -<tool id="cshl_fastx_artifacts_filter" name="Artifacts Filter"> +<tool id="cshl_fastx_artifacts_filter" name="Remove sequencing artifacts"> <description></description> <command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output"</command> <inputs> - <param format="fasta,fastqsolexa" name="input" type="data" label="Library to filter" /> + <param format="fasta,fastqsanger" name="input" type="data" label="Library to filter" /> </inputs> @@ -74,7 +74,12 @@ AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA + +------ +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastx_nucleotides_distribution.xml --- a/tools/fastx_toolkit/fastx_nucleotides_distribution.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastx_nucleotides_distribution.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,9 +1,9 @@ -<tool id="cshl_fastx_nucleotides_distribution" name="Nucleotides Distribution"> - <description>chart</description> +<tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart"> + <description></description> <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command> <inputs> - <param format="txt" name="input" type="data" label="Statistics Text File (output of 'FASTX Statistics' tool)" /> + <param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" /> </inputs> <outputs> @@ -23,44 +23,28 @@ **Output Examples** - - The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT** .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png - - - - - - In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...** .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png - - - - - - - The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem): .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png - - - - - - - But most of the time, the chart will look rather random: .. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastx_quality_statistics.xml --- a/tools/fastx_toolkit/fastx_quality_statistics.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastx_quality_statistics.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="cshl_fastx_quality_statistics" name="Quality Statistics"> +<tool id="cshl_fastx_quality_statistics" name="Compute quality statistics"> <description></description> <command>zcat -f $input | fastx_quality_stats -o $output -Q $offset</command> @@ -55,51 +55,20 @@ * N_Count = Count of 'N' nucleotides found in this column. +For example:: + 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 + 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 + 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 + 4 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 + 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 + +------ +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. - -**Output Example**:: - - column count min max sum mean Q1 med Q3 IQR lW rW A_Count C_Count G_Count T_Count N_Count - 1 6362991 -4 40 250734117 39.41 40 40 40 0 40 40 1396976 1329101 678730 2958184 0 - 2 6362991 -5 40 250531036 39.37 40 40 40 0 40 40 1786786 1055766 1738025 1782414 0 - 3 6362991 -5 40 248722469 39.09 40 40 40 0 40 40 2296384 984875 1443989 1637743 0 - 4 6362991 -5 40 247654797 38.92 40 40 40 0 40 40 1683197 1410855 1722633 1546306 0 - 5 6362991 -4 40 248214827 39.01 40 40 40 0 40 40 2536861 1167423 1248968 1409739 0 - 6 6362991 -5 40 248499903 39.05 40 40 40 0 40 40 1598956 1236081 1568608 1959346 0 - 7 6362991 -4 40 247719760 38.93 40 40 40 0 40 40 1692667 1822140 1496741 1351443 0 - 8 6362991 -5 40 245745205 38.62 40 40 40 0 40 40 2230936 1343260 1529928 1258867 0 - 9 6362991 -5 40 245766735 38.62 40 40 40 0 40 40 1702064 1306257 1336511 2018159 0 - 10 6362991 -5 40 245089706 38.52 40 40 40 0 40 40 1519917 1446370 1450995 1945709 0 - 11 6362991 -5 40 242641359 38.13 40 40 40 0 40 40 1717434 1282975 1387804 1974778 0 - 12 6362991 -5 40 242026113 38.04 40 40 40 0 40 40 1662872 1202041 1519721 1978357 0 - 13 6362991 -5 40 238704245 37.51 40 40 40 0 40 40 1549965 1271411 1973291 1566681 1643 - 14 6362991 -5 40 235622401 37.03 40 40 40 0 40 40 2101301 1141451 1603990 1515774 475 - 15 6362991 -5 40 230766669 36.27 40 40 40 0 40 40 2344003 1058571 1440466 1519865 86 - 16 6362991 -5 40 224466237 35.28 38 40 40 2 35 40 2203515 1026017 1474060 1651582 7817 - 17 6362991 -5 40 219990002 34.57 34 40 40 6 25 40 1522515 1125455 2159183 1555765 73 - 18 6362991 -5 40 214104778 33.65 30 40 40 10 15 40 1479795 2068113 1558400 1249337 7346 - 19 6362991 -5 40 212934712 33.46 30 40 40 10 15 40 1432749 1231352 1769799 1920093 8998 - 20 6362991 -5 40 212787944 33.44 29 40 40 11 13 40 1311657 1411663 2126316 1513282 73 - 21 6362991 -5 40 211369187 33.22 28 40 40 12 10 40 1887985 1846300 1300326 1318380 10000 - 22 6362991 -5 40 213371720 33.53 30 40 40 10 15 40 542299 3446249 516615 1848190 9638 - 23 6362991 -5 40 221975899 34.89 36 40 40 4 30 40 347679 1233267 926621 3855355 69 - 24 6362991 -5 40 194378421 30.55 21 40 40 19 -5 40 433560 674358 3262764 1992242 67 - 25 6362991 -5 40 199773985 31.40 23 40 40 17 -2 40 944760 325595 1322800 3769641 195 - 26 6362991 -5 40 179404759 28.20 17 34 40 23 -5 40 3457922 156013 1494664 1254293 99 - 27 6362991 -5 40 163386668 25.68 13 28 40 27 -5 40 1392177 281250 3867895 821491 178 - 28 6362991 -5 40 156230534 24.55 12 25 40 28 -5 40 907189 981249 4174945 299437 171 - 29 6362991 -5 40 163236046 25.65 13 28 40 27 -5 40 1097171 3418678 1567013 280008 121 - 30 6362991 -5 40 151309826 23.78 12 23 40 28 -5 40 3514775 2036194 566277 245613 132 - 31 6362991 -5 40 141392520 22.22 10 21 40 30 -5 40 1569000 4571357 124732 97721 181 - 32 6362991 -5 40 143436943 22.54 10 21 40 30 -5 40 1453607 4519441 38176 351107 660 - 33 6362991 -5 40 114269843 17.96 6 14 30 24 -5 40 3311001 2161254 155505 734297 934 - 34 6362991 -5 40 140638447 22.10 10 20 40 30 -5 40 1501615 1637357 18113 3205237 669 - 35 6362991 -5 40 138910532 21.83 10 20 40 30 -5 40 1532519 3495057 23229 1311834 352 - 36 6362991 -5 40 117158566 18.41 7 15 30 23 -5 40 4074444 1402980 63287 822035 245 - + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> -</tool> + </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastx_renamer.xml --- a/tools/fastx_toolkit/fastx_renamer.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastx_renamer.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,5 +1,5 @@ -<tool id="cshl_fastx_renamer" name="Rename" version="0.0.11" > - <description>sequence identifiers</description> +<tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" > + <description></description> <command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v </command> <inputs> @@ -50,7 +50,11 @@ +1 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40 - +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastx_reverse_complement.xml --- a/tools/fastx_toolkit/fastx_reverse_complement.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastx_reverse_complement.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,5 +1,5 @@ <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement"> - <description>sequences</description> + <description></description> <command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command> <inputs> <param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" /> @@ -47,6 +47,11 @@ TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA +CSHL_1_FC42AGWWWXX:8:1:3:740 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33 +------ +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + </help> </tool> diff -r 97381671a8e7 -r e9104d403af7 tools/fastx_toolkit/fastx_trimmer.xml --- a/tools/fastx_toolkit/fastx_trimmer.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/fastx_toolkit/fastx_trimmer.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,9 +1,9 @@ -<tool id="cshl_fastx_trimmer" name="Trim"> - <description>sequences</description> +<tool id="cshl_fastx_trimmer" name="Trim sequences"> + <description></description> <command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output</command> <inputs> - <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" /> + <param format="fasta,fastasanger" name="input" type="data" label="Library to clip" /> <param name="first" size="4" type="integer" value="1"> <label>First base to keep</label> @@ -65,6 +65,12 @@ >2-1 AGGCT + ------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + </help> </tool>  diff -r 97381671a8e7 -r e9104d403af7 tools/metag_tools/short_reads_figure_score.xml --- a/tools/metag_tools/short_reads_figure_score.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/metag_tools/short_reads_figure_score.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,5 +1,5 @@ -<tool id="quality_score_distribution" name="Build distribution of base quality"> -<description>values</description> +<tool id="quality_score_distribution" name="Build base quality distribution"> +<description></description> <command interpreter="python">short_reads_figure_score.py $input1 $output1 </command> diff -r 97381671a8e7 -r e9104d403af7 tools/metag_tools/short_reads_trim_seq.xml --- a/tools/metag_tools/short_reads_trim_seq.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/metag_tools/short_reads_trim_seq.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,5 +1,5 @@ <tool id="trim_reads" name="Select high quality segments" version="1.0.0"> -<description>from short reads</description> +<description></description> <command interpreter="python"> short_reads_trim_seq.py $trim $length $output1 $input1 $input2 $sequencing_method_choice.input3 diff -r 97381671a8e7 -r e9104d403af7 tools/metag_tools/split_paired_reads.xml --- a/tools/metag_tools/split_paired_reads.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/metag_tools/split_paired_reads.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,5 +1,5 @@ -<tool id="split_paired_reads" name="Split" version="1.0.0"> - <description>paired-end reads into two ends</description> +<tool id="split_paired_reads" name="Split paired end reads" version="1.0.0"> + <description></description> <command interpreter="python"> split_paired_reads.py $input $output1 $output2 </command> diff -r 97381671a8e7 -r e9104d403af7 tools/solid_tools/solid_qual_boxplot.xml --- a/tools/solid_tools/solid_qual_boxplot.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/solid_tools/solid_qual_boxplot.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="solid_qual_boxplot" name="Quality Boxplot" version="1.0.0"> +<tool id="solid_qual_boxplot" name="Draw quality score boxplot" version="1.0.0"> <description>for SOLiD data</description> <command interpreter="bash">qualsolid_boxplot_graph.sh -t '$input.name' -i $input -o $output</command> @@ -31,6 +31,10 @@ .. image:: ../static/images/solid_qual.png +------ +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool> diff -r 97381671a8e7 -r e9104d403af7 tools/solid_tools/solid_qual_stats.xml --- a/tools/solid_tools/solid_qual_stats.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/solid_tools/solid_qual_stats.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="solid_qual_stats" name="Quality Statistics" version="1.0.0"> +<tool id="solid_qual_stats" name="Compute quality statistics" version="1.0.0"> <description>for SOLiD data</description> <command interpreter="python">solid_qual_stats.py $input $output1</command> @@ -60,6 +60,10 @@ 34 6362991 2 29 140638447 12.10 3 10 25 22 2 29 35 6362991 2 29 138910532 11.83 3 10 25 22 2 29 +------ +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ </help> </tool> diff -r 97381671a8e7 -r e9104d403af7 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,5 +1,5 @@ -<tool id="bowtie_wrapper" name="Bowtie" version="1.0.0"> - <description> fast alignment of reads against reference sequence </description> +<tool id="bowtie_wrapper" name="Map with Bowtie" version="1.0.0"> + <description></description> <command interpreter="python"> bowtie_wrapper.py --threads="8" @@ -148,7 +148,7 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> + <param name="indices" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> <options from_file="bowtie_indices.loc"> <column name="value" index="1" /> <column name="name" index="0" /> @@ -215,7 +215,7 @@ <option value="paired">Paired-end</option> </param> <when value="single"> - <param name="input1" type="data" format="fastqsanger" label="FASTQ file" /> + <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <conditional name="params"> <param name="settings_type" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> <option value="pre_set">Commonly used</option> @@ -272,8 +272,8 @@ </conditional>  </when>  <when value="paired"> - <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" /> - <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" /> + <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> <conditional name="params"> <param name="settings_type" type="select" label="Bowtie settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> <option value="pre_set">Commonly used</option> diff -r 97381671a8e7 -r e9104d403af7 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Mon Sep 21 20:13:20 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Tue Sep 22 08:59:36 2009 -0400 @@ -1,5 +1,5 @@ -<tool id="bwa_wrapper" name="BWA" version="1.0.1"> - <description> fast mapping of reads against reference sequence</description> +<tool id="bwa_wrapper" name="Map with BWA" version="1.0.1"> + <description></description> <command interpreter="python"> bwa_wrapper.py --threads="8" @@ -76,7 +76,7 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> + <param name="indices" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> <options from_file="sequence_index_color.loc"> <column name="value" index="1" /> <column name="name" index="0" /> @@ -116,11 +116,11 @@ <option value="paired">Paired-end</option> </param> <when value="single"> - <param name="input1" type="data" format="fastqsanger" label="FASTQ file" /> + <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> </when> <when value="paired"> - <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" /> - <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" /> + <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> </when> </conditional> <conditional name="params">

1 0

[hg] galaxy 2744: prepare for new trackster
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/97381671a8e7 changeset: 2744:97381671a8e7 user: Kanwei Li <kanwei(a)gmail.com> date: Mon Sep 21 20:13:20 2009 -0400 description: prepare for new trackster 5 file(s) affected in this change: .hgignore lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py lib/galaxy/datatypes/data.py lib/galaxy/datatypes/registry.py lib/galaxy/web/controllers/tracks.py diffs (115 lines): diff -r ce15d5e5b6ad -r 97381671a8e7 .hgignore --- a/.hgignore Mon Sep 21 17:02:26 2009 -0400 +++ b/.hgignore Mon Sep 21 20:13:20 2009 -0400 @@ -27,3 +27,6 @@ # Project files *.kpf + +# Chrom len files +*.len diff -r ce15d5e5b6ad -r 97381671a8e7 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Mon Sep 21 17:02:26 2009 -0400 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Mon Sep 21 20:13:20 2009 -0400 @@ -3,7 +3,7 @@ from __future__ import division import sys - +from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.arrays.array_tree import * from bx.arrays.wiggle import IntervalReader diff -r ce15d5e5b6ad -r 97381671a8e7 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Mon Sep 21 17:02:26 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Mon Sep 21 20:13:20 2009 -0400 @@ -223,7 +223,7 @@ """Returns available converters by type for this dataset""" return datatypes_registry.get_converters_by_datatype(original_dataset.ext) def find_conversion_destination( self, dataset, accepted_formats, datatypes_registry, **kwd ): - """Returns ( target_ext, exisiting converted dataset )""" + """Returns ( target_ext, existing converted dataset )""" return datatypes_registry.find_conversion_destination_for_dataset_by_extensions( dataset, accepted_formats, **kwd ) def convert_dataset(self, trans, original_dataset, target_type, return_output = False, visible = True ): """This function adds a job to the queue to convert a dataset to another type. Returns a message about success/failure.""" diff -r ce15d5e5b6ad -r 97381671a8e7 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Sep 21 17:02:26 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Mon Sep 21 20:13:20 2009 -0400 @@ -211,7 +211,7 @@ except KeyError: #datatype was never declared mimetype = 'application/octet-stream' - self.log.warning('unkown mimetype in data factory %s' % ext) + self.log.warning('unknown mimetype in data factory %s' % ext) return mimetype def get_datatype_by_extension(self, ext ): @@ -265,10 +265,10 @@ tool_xml_text = """ <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.0" tool_type="set_metadata"> <type class="SetMetadataTool" module="galaxy.tools"/> - <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/> - <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command> + <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/> + <command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command> <inputs> - <param format="data" name="input1" type="data" label="File to set metadata on."/> + <param format="data" name="input1" type="data" label="File to set metadata on."/> <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/> <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/> </inputs> @@ -326,7 +326,7 @@ return None def find_conversion_destination_for_dataset_by_extensions( self, dataset, accepted_formats, converter_safe = True ): - """Returns ( target_ext, exisiting converted dataset )""" + """Returns ( target_ext, existing converted dataset )""" for convert_ext in self.get_converters_by_datatype( dataset.ext ): if isinstance( self.get_datatype_by_extension( convert_ext ), accepted_formats ): datasets = dataset.get_converted_files_by_type( convert_ext ) @@ -347,12 +347,12 @@ rval = {} for ext, d_type in self.datatypes_by_extension.iteritems(): inputs = [] - for meta_name, meta_spec in d_type.metadata_spec.iteritems(): - if meta_spec.set_in_upload: + for meta_name, meta_spec in d_type.metadata_spec.iteritems(): + if meta_spec.set_in_upload: help_txt = meta_spec.desc if not help_txt or help_txt == meta_name: help_txt = "" - inputs.append( '<param type="text" name="%s" label="Set metadata value for "%s"" value="%s" help="%s"/>' % ( meta_name, meta_name, meta_spec.default, help_txt ) ) + inputs.append( '<param type="text" name="%s" label="Set metadata value for "%s"" value="%s" help="%s"/>' % ( meta_name, meta_name, meta_spec.default, help_txt ) ) rval[ ext ] = "\n".join( inputs ) if 'auto' not in rval and 'txt' in rval: #need to manually add 'auto' datatype rval[ 'auto' ] = rval[ 'txt' ] diff -r ce15d5e5b6ad -r 97381671a8e7 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Mon Sep 21 17:02:26 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Mon Sep 21 20:13:20 2009 -0400 @@ -33,7 +33,7 @@ ) # Dataset type required for each track type. This needs to be more flexible, -# there might be mutliple types of indexes that suffice for a given track type. +# there might be multiple types of indexes that suffice for a given track type. track_type_to_dataset_type = { "line": "array_tree" } @@ -158,7 +158,7 @@ converted_dataset_type = track_type_to_dataset_type[track_type] converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type ) # If at this point we still don't have an `array_tree_dataset`, there - # is now way we can display this data as an array tree + # is no way we can display this data as an array tree if converted_dataset is None: return messages.NO_DATA # Need to check states again for the converted version @@ -186,7 +186,7 @@ return dataset # See if we can convert the dataset if type not in dataset.get_converter_types(): - log.debug( "Conversion from '%s' to '%d' not possible", dataset.extension, type ) + log.debug( "Conversion from '%s' to '%s' not possible", dataset.extension, type ) return None # See if converted dataset already exists converted_datasets = dataset.get_converted_files_by_type( type )

1 0

[hg] galaxy 2742: Merge with ad4f25a155f02f31edabc5baa822a92610e...
by Nate Coraor 25 Sep '09

25 Sep '09

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="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

1 0

[hg] galaxy 2741: Removed print stmts in listener
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2f2c07fa1a39 changeset: 2741:2f2c07fa1a39 user: rc date: Mon Sep 21 15:40:58 2009 -0400 description: Removed print stmts in listener 1 file(s) affected in this change: scripts/galaxy_messaging/amqp_consumer.py diffs (43 lines): diff -r df1f5b739a53 -r 2f2c07fa1a39 scripts/galaxy_messaging/amqp_consumer.py --- a/scripts/galaxy_messaging/amqp_consumer.py Mon Sep 21 14:45:56 2009 -0400 +++ b/scripts/galaxy_messaging/amqp_consumer.py Mon Sep 21 15:40:58 2009 -0400 @@ -26,6 +26,10 @@ from amqplib import client_0_8 as amqp +import logging +logging.basicConfig(level=logging.DEBUG) +log = logging.getLogger( 'GalaxyAMQP' ) + galaxy_config_file = 'universe_wsgi.ini' global dbconnstr @@ -42,16 +46,16 @@ return rc def recv_callback(msg): - #print 'Received: ' + msg.body + ' from channel #' + str(msg.channel.channel_id) dom = xml.dom.minidom.parseString(msg.body) barcode = get_value(dom, 'barcode') state = get_value(dom, 'state') - print barcode, state + log.debug('Barcode: '+barcode) + log.debug('State: '+state) # update the galaxy db galaxy = GalaxyDbInterface(dbconnstr) sample_id = galaxy.get_sample_id(field_name='bar_code', value=barcode) if sample_id == -1: - print 'Invalid barcode.' + log.debug('Invalid barcode.') return galaxy.change_state(sample_id, state) @@ -63,7 +67,7 @@ amqp_config = {} for option in config.options("galaxy:amqp"): amqp_config[option] = config.get("galaxy:amqp", option) - print amqp_config + log.debug(str(amqp_config)) conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], userid=amqp_config['userid'], password=amqp_config['password'],

1 0

[hg] galaxy 2743: Modified sort to allow sorting by multiple col...
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ce15d5e5b6ad changeset: 2743:ce15d5e5b6ad user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Mon Sep 21 17:02:26 2009 -0400 description: Modified sort to allow sorting by multiple columns 5 file(s) affected in this change: test-data/sort_in1.bed test-data/sort_out1.bed test-data/sort_out2.bed tools/filters/sorter.py tools/filters/sorter.xml diffs (304 lines): diff -r 46852d01ff16 -r ce15d5e5b6ad test-data/sort_in1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort_in1.bed Mon Sep 21 17:02:26 2009 -0400 @@ -0,0 +1,29 @@ +chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, +chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, +chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, +chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, +chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, +chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, +chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, +chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, +chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, +chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, +chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, +chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790, +chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, +chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, +chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, +chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, +chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, +chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, +chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, +chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, +chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, +chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, +chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, +chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, +chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825, +chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607, +chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759, +chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, +chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, diff -r 46852d01ff16 -r ce15d5e5b6ad test-data/sort_out1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort_out1.bed Mon Sep 21 17:02:26 2009 -0400 @@ -0,0 +1,29 @@ +chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, +chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, +chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, +chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, +chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, +chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, +chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, +chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, +chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, +chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, +chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, +chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790, +chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, +chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, +chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, +chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, +chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, +chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, +chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, +chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, +chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, +chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, +chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, +chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, +chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825, +chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607, +chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759, +chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, +chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, diff -r 46852d01ff16 -r ce15d5e5b6ad test-data/sort_out2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort_out2.bed Mon Sep 21 17:02:26 2009 -0400 @@ -0,0 +1,29 @@ +chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, +chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, +chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, +chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, +chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, +chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, +chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, +chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, +chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, +chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, +chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, +chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790, +chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, +chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, +chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, +chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, +chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, +chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, +chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, +chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, +chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, +chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, +chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, +chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, +chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825, +chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607, +chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759, +chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, +chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, diff -r 46852d01ff16 -r ce15d5e5b6ad tools/filters/sorter.py --- a/tools/filters/sorter.py Mon Sep 21 15:43:38 2009 -0400 +++ b/tools/filters/sorter.py Mon Sep 21 17:02:26 2009 -0400 @@ -1,113 +1,32 @@ -# Filename: sorter.py -# Author: Ian N. Schenck -# Version: 8/22/2005 -# # This script sorts a file based on the inputs: # -cols - column to sort on -# -order - ASC or DESC-ing order +# -order - ASC- or DESCending order # -i - input filename # -o - output filename -import string -import sys -import re -import commands -from os import environ +import os, re, string, sys -def getopts(argv): - opts = {} - while argv: - if argv[0][0] == '-': - opts[argv[0]] = argv[1] - argv = argv[2:] - else: - argv = argv[1:] - return opts +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() def main(): - args = sys.argv[1:] + try: + inputfile = sys.argv[1] + outputfile = '-o %s' % sys.argv[2] + order = ('', '-r')[sys.argv[3] == 'DESC'] + sort_type = ('','-n')[sys.argv[4] == 'num'] + columns = sys.argv[5:] + cols = [ '-k%s,%s'%(n, n) for n in columns ] + except Exception, ex: + stop_err('Error parsing input parameters\n' + str(ex)) + # Launch sort. + cmd = "sort -f -t $'\t' %s %s %s %s %s" % (sort_type, ' '.join(cols), order, outputfile, inputfile) try: - opts = getopts(args) - except IndexError: - print "Usage:" - print " -o Output filename" - print " -i Input filename" - print " -cols Column to sort (base 1)" - print " -order ASC or DESC" - print " -style num or alpha" - return 0 - - outputfile = opts.get("-o") - if outputfile == None: - print "No output file specified." - return -1 - - inputfile = opts.get("-i") - if inputfile == None: - print "No input file specified." - return -2 - - column = opts.get("-cols") - if column == None or column == 'None': - print "Sort column not specified." - return -3 - - order = opts.get("-order") - if order == None: - print "Sort order not specified." - return -4 - - style = opts.get("-style") - if style == None: - style = "num" - - # At this point, all command line options have been collected. - # Verify arguments are valid. - - fileRegEx = re.compile("^[A-Za-z0-9./\-_]+$") - numberRegEx = re.compile("^[0-9]+$") - sortRegEx = re.compile("^(ASC|DESC)$") - if not fileRegEx.match(outputfile): - print "Illegal output filename." - return -5 - if not fileRegEx.match(inputfile): - print "Illegal input filename." - return -6 - if not numberRegEx.match(column): - print "Column number not an integer." - return -7 - if not sortRegEx.match(order): - print "Sort order must be ASCending or DESCending." - return -8 - - # Check sort column against max columns in input file. - - column = string.atoi(column) - if column > len( open(inputfile).readline().split('\t') ): - print "Column "+str(column)+" does not exist." - return -9 - - # Everything is kosher. - - if order == "DESC": - order = " -r" - else: - order = "" - - if style == "num": - style = " -n " - else: - style = " " - - # Launch sort. - - environ['LC_ALL'] = 'POSIX' - commandline = "sort -f"+style+"-k "+str(column)+" -t $'\t' -o "+outputfile+" "+inputfile+order - - errorcode, stdout = commands.getstatusoutput(commandline) - - return errorcode + os.system(cmd) + except Exception, ex: + stop_err('Error running sort command\n' + str(ex)) if __name__ == "__main__": main() diff -r 46852d01ff16 -r ce15d5e5b6ad tools/filters/sorter.xml --- a/tools/filters/sorter.xml Mon Sep 21 15:43:38 2009 -0400 +++ b/tools/filters/sorter.xml Mon Sep 21 17:02:26 2009 -0400 @@ -1,14 +1,27 @@ <tool id="sort1" name="Sort" version="1.0.1"> <description>data in ascending or descending order</description> - <command interpreter="python">sorter.py -i $input -o $out_file1 -cols $column -order $order -style $style</command> + <command interpreter="python"> + sorter.py + $input + $out_file1 + $order + $style + $firstcol + #for $col in $column_set: + ${col.column} + #end for + </command> <inputs> <param format="tabular" name="input" type="data" label="Sort Query" /> - <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> + <param name="firstcol" label="on column" type="data_column" data_ref="input" accept_default="true" /> + <repeat name="column_set" title="Column selection"> + <param name="column" label="on column" type="data_column" data_ref="input" accept_default="true" /> + </repeat> <param name="order" type="select" label="in"> <option value="DESC">Descending order</option> <option value="ASC">Ascending order</option> </param> - <param name="style" type="select" label="Flavor"> + <param name="style" type="select" label="with flavor"> <option value="num">Numerical sort</option> <option value="alpha">Alphabetical sort</option> </param> @@ -18,18 +31,20 @@ </outputs> <tests> <test> - <param name="input" value="1.bed"/> - <param name="column" value="1"/> + <param name="input" value="sort_in1.bed"/> + <param name="firstcol" value="1"/> + <param name="column" value="3" /> <param name="order" value="ASC"/> <param name="style" value="num"/> - <output name="out_file1" file="sort1_num.bed"/> + <output name="out_file1" file="sort_out1.bed"/> </test> <test> - <param name="input" value="7.bed"/> + <param name="input" value="sort_in1.bed"/> + <param name="firstcol" value="3" /> <param name="column" value="1"/> <param name="order" value="ASC"/> <param name="style" value="alpha"/> - <output name="out_file1" file="sort1_alpha.bed"/> + <output name="out_file1" file="sort_out2.bed"/> </test> </tests> <help> @@ -42,7 +57,7 @@ **Syntax** -This tool sorts the dataset on any column in either ascending or descending order. +This tool sorts the dataset on any number of columns in either ascending or descending order (all columns will be ascending or descending). * Numerical sort orders numbers by their magnitude, ignores all characters besides numbers, and evaluates a string of numbers to the value they signify. * Alphabetical sort is a phonebook type sort based on the conventional order of letters in an alphabet. Each nth letter is compared with the nth letter of other words in the list, starting at the first letter of each word and advancing to the second, third, fourth, and so on, until the order is established. Therefore, in an alphabetical sort, 2 comes after 100 (1 < 2).

1 0

[hg] galaxy 2739: galaxy amqp listener now runs as a daemon
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/df1f5b739a53 changeset: 2739:df1f5b739a53 user: rc date: Mon Sep 21 14:45:56 2009 -0400 description: galaxy amqp listener now runs as a daemon 1 file(s) affected in this change: run_galaxy_listener.sh diffs (11 lines): diff -r 2b730844747b -r df1f5b739a53 run_galaxy_listener.sh --- a/run_galaxy_listener.sh Mon Sep 21 12:41:39 2009 -0400 +++ b/run_galaxy_listener.sh Mon Sep 21 14:45:56 2009 -0400 @@ -1,3 +1,4 @@ #!/bin/sh -python scripts/galaxy_messaging/amqp_consumer.py \ No newline at end of file +cd `dirname $0` +python scripts/galaxy_messaging/amqp_consumer.py >> galaxy_listener.log 2>&1 \ No newline at end of file

1 0

[hg] galaxy 2740: Tweaks plus reducing size of Assaf's icons
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ad4f25a155f0 changeset: 2740:ad4f25a155f0 user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Mon Sep 21 15:40:22 2009 -0400 description: Tweaks plus reducing size of Assaf's icons 13 file(s) affected in this change: static/fastx_icons/barcode_splitter_output_example.png static/fastx_icons/fasta_clipping_histogram_1.png static/fastx_icons/fasta_clipping_histogram_2.png static/fastx_icons/fastq_nucleotides_distribution_1.png static/fastx_icons/fastq_nucleotides_distribution_2.png static/fastx_icons/fastq_nucleotides_distribution_3.png static/fastx_icons/fastq_nucleotides_distribution_4.png static/fastx_icons/fastq_quality_boxplot_1.png static/fastx_icons/fastq_quality_boxplot_2.png static/fastx_icons/fastq_quality_boxplot_3.png static/fastx_icons/fastx_clipper_example.png tool_conf.xml.sample tools/samtools/sam2interval.xml diffs (59 lines): diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/barcode_splitter_output_example.png Binary file static/fastx_icons/barcode_splitter_output_example.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fasta_clipping_histogram_1.png Binary file static/fastx_icons/fasta_clipping_histogram_1.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fasta_clipping_histogram_2.png Binary file static/fastx_icons/fasta_clipping_histogram_2.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastq_nucleotides_distribution_1.png Binary file static/fastx_icons/fastq_nucleotides_distribution_1.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastq_nucleotides_distribution_2.png Binary file static/fastx_icons/fastq_nucleotides_distribution_2.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastq_nucleotides_distribution_3.png Binary file static/fastx_icons/fastq_nucleotides_distribution_3.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastq_nucleotides_distribution_4.png Binary file static/fastx_icons/fastq_nucleotides_distribution_4.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastq_quality_boxplot_1.png Binary file static/fastx_icons/fastq_quality_boxplot_1.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastq_quality_boxplot_2.png Binary file static/fastx_icons/fastq_quality_boxplot_2.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastq_quality_boxplot_3.png Binary file static/fastx_icons/fastq_quality_boxplot_3.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 static/fastx_icons/fastx_clipper_example.png Binary file static/fastx_icons/fastx_clipper_example.png has changed diff -r df1f5b739a53 -r ad4f25a155f0 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Sep 21 14:45:56 2009 -0400 +++ b/tool_conf.xml.sample Mon Sep 21 15:40:22 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="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 df1f5b739a53 -r ad4f25a155f0 tools/samtools/sam2interval.xml --- a/tools/samtools/sam2interval.xml Mon Sep 21 14:45:56 2009 -0400 +++ b/tools/samtools/sam2interval.xml Mon Sep 21 15:40:22 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

1 0

[hg] galaxy 2737: Galaxy AMQP messaging now uses amqp & sqlalche...
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/7a4e6f19aa17 changeset: 2737:7a4e6f19aa17 user: rc date: Mon Sep 21 12:06:33 2009 -0400 description: Galaxy AMQP messaging now uses amqp & sqlalchemy eggs 2 file(s) affected in this change: scripts/galaxy_messaging/amqp_consumer.py scripts/galaxy_messaging/galaxydb_interface.py diffs (58 lines): diff -r f2e5b1725b50 -r 7a4e6f19aa17 scripts/galaxy_messaging/amqp_consumer.py --- a/scripts/galaxy_messaging/amqp_consumer.py Mon Sep 21 11:21:35 2009 -0400 +++ b/scripts/galaxy_messaging/amqp_consumer.py Mon Sep 21 12:06:33 2009 -0400 @@ -9,13 +9,23 @@ this script can be run to receive messages and update the Galaxy database accordingly ''' - -from amqplib import client_0_8 as amqp import ConfigParser -import sys +import sys, os import optparse import xml.dom.minidom from galaxydb_interface import GalaxyDbInterface + +assert sys.version_info[:2] >= ( 2, 4 ) +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path + +from galaxy import eggs +import pkg_resources +pkg_resources.require( "amqplib" ) + +from amqplib import client_0_8 as amqp + galaxy_config_file = 'universe_wsgi.ini' global dbconnstr diff -r f2e5b1725b50 -r 7a4e6f19aa17 scripts/galaxy_messaging/galaxydb_interface.py --- a/scripts/galaxy_messaging/galaxydb_interface.py Mon Sep 21 11:21:35 2009 -0400 +++ b/scripts/galaxy_messaging/galaxydb_interface.py Mon Sep 21 12:06:33 2009 -0400 @@ -1,13 +1,22 @@ #/usr/bin/python -from sqlalchemy import * -from sqlalchemy.orm import sessionmaker from datetime import datetime, timedelta import sys import optparse import os import time import logging + +assert sys.version_info[:2] >= ( 2, 4 ) +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[1:] ) # remove scripts/ from the path +sys.path = new_path +from galaxy import eggs +import pkg_resources +#pkg_resources.require( "psycopg2 >= 2.0.6" ) +pkg_resources.require( "SQLAlchemy >= 0.4" ) +from sqlalchemy import * +from sqlalchemy.orm import sessionmaker logging.basicConfig(level=logging.DEBUG) log = logging.getLogger( 'GalaxyDbInterface' )

1 0

[hg] galaxy 2736: Add amqplib egg
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f2e5b1725b50 changeset: 2736:f2e5b1725b50 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Sep 21 11:21:35 2009 -0400 description: Add amqplib egg 1 file(s) affected in this change: eggs.ini diffs (19 lines): diff -r 12e6192f6201 -r f2e5b1725b50 eggs.ini --- a/eggs.ini Mon Sep 21 10:49:17 2009 -0400 +++ b/eggs.ini Mon Sep 21 11:21:35 2009 -0400 @@ -25,6 +25,7 @@ guppy = 0.1.8 [eggs:noplatform] +amqplib = 0.6.1 Beaker = 1.4 docutils = 0.4 elementtree = 1.2.6_20050316 @@ -73,6 +74,7 @@ python_lzo = http://www.oberhumer.com/opensource/lzo/download/LZO-v1/python-lzo-1.08.tar… http://www.oberhumer.com/opensource/lzo/download/LZO-v1/lzo-1.08.tar.gz threadframe = http://www.majid.info/python/threadframe/threadframe-0.2.tar.gz guppy = http://pypi.python.org/packages/source/g/guppy/guppy-0.1.8.tar.gz +amqplib = http://py-amqplib.googlecode.com/files/amqplib-0.6.1.tgz Beaker = http://cheeseshop.python.org/packages/source/B/Beaker/Beaker-1.4.tar.gz docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz

1 0

[hg] galaxy 2738: added psycopg2 import stmt in galaxy_interface.py
by Nate Coraor 25 Sep '09

25 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2b730844747b changeset: 2738:2b730844747b user: rc date: Mon Sep 21 12:41:39 2009 -0400 description: added psycopg2 import stmt in galaxy_interface.py 1 file(s) affected in this change: scripts/galaxy_messaging/galaxydb_interface.py diffs (13 lines): diff -r 7a4e6f19aa17 -r 2b730844747b scripts/galaxy_messaging/galaxydb_interface.py --- a/scripts/galaxy_messaging/galaxydb_interface.py Mon Sep 21 12:06:33 2009 -0400 +++ b/scripts/galaxy_messaging/galaxydb_interface.py Mon Sep 21 12:41:39 2009 -0400 @@ -13,7 +13,8 @@ sys.path = new_path from galaxy import eggs import pkg_resources -#pkg_resources.require( "psycopg2 >= 2.0.6" ) +pkg_resources.require( "psycopg2" ) +import psycopg2 pkg_resources.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import * from sqlalchemy.orm import sessionmaker

1 0