Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 81a0cbf4721d7279e3a5b901e1646380d797635b
https://github.com/galaxyproject/galaxy/commit/81a0cbf4721d7279e3a5b901e164…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-13 (Tue, 13 Dec 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
Log Message:
-----------
Update datatype converter tools
- dos2unix
- Fix indentation
- Add missing tool version
- Remove deprecated <page> elements
- Remove deprecated 'interpreter' attribute of <command>
- Quote some data parameters in <command>
- Remove some duplicated requirement
Commit: ac8450f013284bc5b8502cfec0d64e809390ce02
https://github.com/galaxyproject/galaxy/commit/ac8450f013284bc5b8502cfec0d6…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2016-12-13 (Tue, 13 Dec 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
Log Message:
-----------
Add CDATA. Use && to concatenate commands. Quote $chromInfo
Commit: cf7119c474e294eae79320fa5a51e5cdb5fa5835
https://github.com/galaxyproject/galaxy/commit/cf7119c474e294eae79320fa5a51…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-12-13 (Tue, 13 Dec 2016)
Changed paths:
M lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
M lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/bed_to_fli_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.xml
M lib/galaxy/datatypes/converters/bed_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/bed_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/encodepeak_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_bowtie_color_index_converter.xml
M lib/galaxy/datatypes/converters/fasta_to_len.xml
M lib/galaxy/datatypes/converters/fasta_to_tabular_converter.xml
M lib/galaxy/datatypes/converters/fastq_to_fqtoc.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bed_converter.xml
M lib/galaxy/datatypes/converters/gff_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/gff_to_fli_converter.xml
M lib/galaxy/datatypes/converters/gff_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/gff_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed12_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bed_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/interval_to_coverage.xml
M lib/galaxy/datatypes/converters/interval_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/len_to_linecount.xml
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.xml
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.xml
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.xml
M lib/galaxy/datatypes/converters/maf_to_interval_converter.xml
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.xml
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.xml
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.xml
M lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.xml
M lib/galaxy/datatypes/converters/vcf_bgzip_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_bgzip_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_tabix_converter.xml
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml
M lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml
Log Message:
-----------
Merge pull request #3305 from nsoranzo/converter_tools
Update datatype converter tools
Compare: https://github.com/galaxyproject/galaxy/compare/ad8d48c0a39d...cf7119c474e2