Fix for 'Error Setting BAM Metadata' when input is BAM and selected output format is SAM.
Remove redundant --do_not_build_index parameter.
Add <version_command> .
Improve some parameter help texts.
Remove --cutoff option of bowtie-build (removed since bowtie-0.12.0).
Add <version_command> .
pylint fixes.
Improve some parameter help texts. Add min for some parameters.
Re-add tool_depedencies.xml .

Partially revert commit 7075dc7b72175f573edd6fbc1edfe4cce9694893 .
Remove changeset_revision and toolshed attributes from <repository> in all tool_dependencies.xml files.

This was accomplished with the following command:

find . -name tool_dependencies.xml -print0 | xargs -0 sed -i -e 's/ changeset_revision="[a-z0-9]\{1,\}"//g' -e 's/ toolshed="https\{0,1\}:\/\/toolshed.g2.bx.psu.edu\/\{0,1\}"//g'
Merge pull request #5 from nsoranzo/master

Fixes for various tools and remove revision and toolshed tag from package definitions ...