commit/galaxy-central: dan: Minor tool help updates.
1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d57affe81874/ changeset: d57affe81874 user: dan date: 2011-08-25 16:00:09 summary: Minor tool help updates. affected #: 28 files (7.7 KB) --- a/tools/fastq/fastq_combiner.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_combiner.xml Thu Aug 25 10:00:09 2011 -0400 @@ -66,5 +66,12 @@ Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93). Use this tool, for example, to convert 454-type output to FASTQ. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + </help></tool> --- a/tools/fastq/fastq_filter.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_filter.xml Thu Aug 25 10:00:09 2011 -0400 @@ -307,5 +307,12 @@ Adapter bases in color space reads are excluded from filtering. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_groomer.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_groomer.xml Thu Aug 25 10:00:09 2011 -0400 @@ -358,6 +358,12 @@ Diagram adapted from http://en.wikipedia.org/wiki/FASTQ_format +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + .. _Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16.: http://www.ncbi.nlm.nih.gov/pubmed/20015970 --- a/tools/fastq/fastq_manipulation.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_manipulation.xml Thu Aug 25 10:00:09 2011 -0400 @@ -417,5 +417,13 @@ 2. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "Change Adapter Base" and set **New Adapter** to "" (an empty text field). 3. Click **Add new Manipulate Reads**, change **Manipulate Reads on** to "Sequence Content", set **Sequence Manipulation Type** to "String Translate" and set **From** to "0123." and **To** to "ACGTN". 4. Click Execute. The new history item will contained double-encoded psuedo-nucleotide space reads. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_masker_by_quality.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_masker_by_quality.xml Thu Aug 25 10:00:09 2011 -0400 @@ -49,5 +49,12 @@ This tool is not available for use on color space (csSanger) formats. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_paired_end_joiner.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_paired_end_joiner.xml Thu Aug 25 10:00:09 2011 -0400 @@ -51,5 +51,12 @@ +HWI-EAS91_1_30788AAXX:7:21:1542:1758 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_paired_end_splitter.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_paired_end_splitter.xml Thu Aug 25 10:00:09 2011 -0400 @@ -52,5 +52,12 @@ +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_stats.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_stats.xml Thu Aug 25 10:00:09 2011 -0400 @@ -60,5 +60,12 @@ Adapter bases in color space reads are excluded from statistics. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_to_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_to_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -29,5 +29,12 @@ This tool converts FASTQ sequencing reads to FASTA sequences. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_to_tabular.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_to_tabular.xml Thu Aug 25 10:00:09 2011 -0400 @@ -90,5 +90,12 @@ Note the sequences and quality strings have been truncated for display purposes in the above tables. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_trimmer.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_trimmer.xml Thu Aug 25 10:00:09 2011 -0400 @@ -109,5 +109,12 @@ Trimming a color space read will cause any adapter base to be lost. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/fastq_trimmer_by_quality.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/fastq_trimmer_by_quality.xml Thu Aug 25 10:00:09 2011 -0400 @@ -134,5 +134,12 @@ Trimming a color space read will cause any adapter base to be lost. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/fastq/tabular_to_fastq.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/fastq/tabular_to_fastq.xml Thu Aug 25 10:00:09 2011 -0400 @@ -33,5 +33,12 @@ This tool attempts to convert a tabular file containing sequencing read data to a FASTQ formatted file. The FASTQ Groomer tool should always be used on the output of this tool. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + + </help></tool> --- a/tools/maf/genebed_maf_to_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/genebed_maf_to_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -87,6 +87,12 @@ * stitches blocks together and resolves overlaps based on alignment score; * outputs alignments in FASTA format. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help></tool> --- a/tools/maf/interval2maf.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/interval2maf.xml Thu Aug 25 10:00:09 2011 -0400 @@ -283,5 +283,12 @@ s species2.chr1 129723925 79 + 229575298 ATGGCGTCGGCCTCCTCCGGGCCGTCGTCTTCGGTCGGTTTTTCATCCTTTGATCCCGCGGTCCCTTCCTGTACCTC------AG s species3.chr3 68255714 76 - 258222147 ATGGCGTCCGCCTCCTCAGGGCCAGCGGC---GGCGGGGTTTTCACCCCTTGATTCCGGGGTCCCTGCCGGTACCGC------AG +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/interval2maf_pairwise.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/interval2maf_pairwise.xml Thu Aug 25 10:00:09 2011 -0400 @@ -39,5 +39,12 @@ .. image:: ./static/images/maf_icons/interval2maf.png +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/interval_maf_to_merged_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -103,5 +103,12 @@ .. image:: ./static/images/maf_icons/stitchMaf.png +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_by_block_number.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_by_block_number.xml Thu Aug 25 10:00:09 2011 -0400 @@ -28,5 +28,13 @@ **What it does** This tool takes a list of block numbers, one per line, and extracts the corresponding MAF blocks from the provided file. Block numbers start at 0. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_filter.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_filter.xml Thu Aug 25 10:00:09 2011 -0400 @@ -191,5 +191,12 @@ You can also provide a size range and limit your output to the MAF blocks which fall within the specified range. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_limit_size.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_limit_size.xml Thu Aug 25 10:00:09 2011 -0400 @@ -24,5 +24,13 @@ **What it does** This tool takes a MAF file and a size range and extracts the MAF blocks which fall within the specified range. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_limit_to_species.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_limit_to_species.xml Thu Aug 25 10:00:09 2011 -0400 @@ -39,6 +39,13 @@ * **Exclude blocks with have only one species** - if this option is set to **YES** all single sequence alignment blocks WILL NOT be returned. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_reverse_complement.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_reverse_complement.xml Thu Aug 25 10:00:09 2011 -0400 @@ -41,5 +41,13 @@ s hg17.chr7 31156555 58 - 158628139 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAATGAATAAACCACAAATT s panTro1.chr6 31691510 58 - 161576975 CCTCTTCCACTATAGACCTCCTTAAACAAAATAATGAAAAACGAATAAACCACAAATT s mm5.chr6 120816549 54 - 149721531 CCTCTTCCACTGAGGAATTTCTTTTTTTAAATGATGAGCAATCAATGAAACG----TT + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_split_by_species.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_split_by_species.xml Thu Aug 25 10:00:09 2011 -0400 @@ -211,6 +211,13 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_stats.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_stats.xml Thu Aug 25 10:00:09 2011 -0400 @@ -108,5 +108,13 @@ ======== =========== ======== where **coverage** is the number of nucleotides divided by the total length of the provided intervals. + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + </help></tool> --- a/tools/maf/maf_thread_for_species.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_thread_for_species.xml Thu Aug 25 10:00:09 2011 -0400 @@ -48,6 +48,11 @@ s hg17.chr7 127471195 389 + 158628139 gtttgccatcttttgctgctctagggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTAAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCATTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG s panTro1.chr6 129885076 389 + 161576975 gtttgccatcttttgctgctcttgggaatccagcagctgtcaccatgtaaacaagcccaggctagaccaGTTACCCTCATCATCTTAGCTGATAGCCAGCCAGCCACCACAGGCAtgagtcaggccatattgctggacccacagaattatgagctaaataaatagtcttgggttaagccactaagttttaggcatagtgtgttatgtaTCTCACAAACATATAAGACTGTGTGTTTGTTGACTGGAGGAAGAGATGCTATAAAGACCACCTTTTGAAACTTCCCAAATACTGCCACTGATGTCCTGATGGAGGTATGAAAACATCCACTAAAATTTGTGGTTTATTCGTTTTTCATTATTTTGTTTAAGGAGGTCTATAGTGGAAGAGG +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ </help> --- a/tools/maf/maf_to_bed.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_to_bed.xml Thu Aug 25 10:00:09 2011 -0400 @@ -123,6 +123,12 @@ 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help><code file="maf_to_bed_code.py"/> --- a/tools/maf/maf_to_fasta.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_to_fasta.xml Thu Aug 25 10:00:09 2011 -0400 @@ -188,6 +188,12 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help></tool> --- a/tools/maf/maf_to_interval.xml Wed Aug 24 17:15:34 2011 -0400 +++ b/tools/maf/maf_to_interval.xml Thu Aug 25 10:00:09 2011 -0400 @@ -121,6 +121,12 @@ - An "i" line containing information about what is in the aligned species DNA before and after the immediately preceding "s" line; - An "e" line containing information about the size of the gap between the alignments that span the current block. +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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