Enhance the genetrack, cwpair2 and repmatch_gff3 tools to include the

help text and images provided by Frank.

See merge request !18

help text and images provided by Frank.

Update the bam_to_scidx .shed.yml file in preparation for release to

open source.

See merge request !17

open source.

Add a feature for hiding / displaying advanced options for the

Repmatch_gff3 tool.

See merge request !16

Repmatch_gff3 tool.

Changes to tool interfaces based on first review by the Pugh/Mahony

labs.

See merge request !15

labs.

Make genetrack require Anaconda 2.3.0 instead of Numpy 1.9.  This does

not change the behavior of the tool, but makes it consistent with the
dependencies for Cwpair2 and Repmatch_gff3.

See merge request !14

not change the behavior of the tool, but makes it consistent with the
dependencies for Cwpair2 and Repmatch_gff3.

Add the bam_to_scidx tool.

See merge request !13

never worked, and eliminate the ability to convert chromosome label
formats to / from Roman in the Genetrack tool since this format was
never used.  Add a .shed.yml file for the bam_to_scidx tool.

Rename the SsccIdx datatype to be ScIdx.

See merge request !12

statistics output files.

Add .shed.yml file sin preparation for submitting to open source.

See merge request !11

Next round of fixes for all 3 tools.  Genetrack must use optparse rather

than the more ideal argparse since Python 2.6 is supported.  A few other
misellaneous fixes for the other 2 tools.  The Pugh lab's idx datatype
now has Galaxy extension ssccidx - the IUC told me that the more generic
idx would not be accepted.

See merge request !10

than the more ideal argparse since Python 2.6 is supported.  A few other
misellaneous fixes for the other 2 tools.  The Pugh lab's idx datatype
now has Galaxy extension ssccidx - the IUC told me that the more generic
idx would not be accepted.

Production-ready version of the cwpair2 tool along with test data for 2

functional tests.  This version of the tool produces the exact output as
the original tool for all match methods and output formats.

See merge request !9

produces the exact output as the original script.  Also add some minor
fixes for the cwpair2 tool.  All 3 tools can be reviewed at any time.

sizes.

functional tests.  This version of the tool produces the exact output as
the original tool for all match methods and output formats.

Push changes to cwpair2 and repmatch_gff3 so Geoffrey can proceed with

repmatch_gff3.

See merge request !8

repmatch_gff3.

More finishing touches on the genetrack tool.

See merge request !7

Enhancements to the genetrack tool to produce an output collection and

add functional tests.  ALl tests pass with planemo, and the test output
datasets do not differ from the output datasets produced by the original
genetrack script on which this tool is based.

See merge request !6

add functional tests.  ALl tests pass with planemo, and the test output
datasets do not differ from the output datasets produced by the original
genetrack script on which this tool is based.

Added smaller input and output test datasets for cwpair2 tool.

See merge request !5

Deleted large test datasets for cwpair2 tool.

See merge request !4