Update README.md

make link to CONTRIBUTING.md clickable
Update CONTRIBUTING.md

Modify language for IUC - I made it sound like that repository is what tool shed authors should aspire to - not sure that is actually a best practice - it might just be best practice for the IUC members themselves.
Update README.md

added links to other repos
Update README.md

added Peter Cock's repos
add gitignore file
Add wrapper updates from Geert Vandeweyer. For more information please see: https://trello.com/c/bfr0jKut. Added small enhancements and the new citation tag.
Remove yield statement from citation tag. I'm so used to macros, Oo.
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'
Specify output ftype="bam" on bowtie2 wrapper get sam output for failing test.
Merge pull request #5 from nsoranzo/master

Fixes for various tools and remove revision and toolshed tag from package definitions ...
Merge pull request #6 from jmchilton/bowtie2_output_type

Specify output ftype="bam" on bowtie2 wrapper get sam output for failing test.