1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/6591b6ebfb4e/ changeset: 6591b6ebfb4e user: jgoecks date: 2012-12-07 16:33:39 summary: Converter enhancements: (a) add bam to bigwig converter; (b) update datatypes.conf.sample to include new converter (disabled by default and documented with requirements) and remove unneeded dependency for bam to summary tree converter; and (c) remove deprecated page tags from bedgraph to bigwig converter. affected #: 3 files

diff -r 8305907fa2312da14cf4d500fba1675a169b5517 -r 6591b6ebfb4ea56118941deef03855412c2c00fd datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -7,7 +7,12 @@ <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/><datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"><converter file="bam_to_bai.xml" target_datatype="bai"/> - <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree" depends_on="bai"/> + <converter file="bam_to_summary_tree_converter.xml" target_datatype="summary_tree"/> + <!-- + Caution: (a) this converter requires bedtools to be installed and (b) it is very memory intensive and + is not recommended for most laptops/desktops. + <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/> + --><display file="ucsc/bam.xml" /><display file="ensembl/ensembl_bam.xml" /><display file="igv/bam.xml" />

diff -r 8305907fa2312da14cf4d500fba1675a169b5517 -r 6591b6ebfb4ea56118941deef03855412c2c00fd lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml --- /dev/null +++ b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml @@ -0,0 +1,14 @@ +<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.0" hidden="true"> + <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> + <command> + bedtools genomecov -bg -split -ibam $input -g $chromInfo | wigToBigWig stdin $chromInfo $output + </command> + <inputs> + <param format="bam" name="input" type="data" label="Choose BAM file"/> + </inputs> + <outputs> + <data format="bigwig" name="output"/> + </outputs> + <help> + </help> +</tool>

diff -r 8305907fa2312da14cf4d500fba1675a169b5517 -r 6591b6ebfb4ea56118941deef03855412c2c00fd lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml @@ -2,9 +2,7 @@ <!-- Used internally to generate track indexes --><command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command><inputs> - <page><param format="bedgraph" name="input" type="data" label="Choose wiggle"/> - </page></inputs><outputs><data format="bigwig" name="output"/>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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