Executing dockerized tools in phpstorm

I have recently converted my development environment to operate inside a container, and i have managed to get everything to work apart from one thing. external tools 

Every time I  try to execute the my function inside the docker container PHPStorm tells me the command is not found.  I have it setup as a tool

<toolSet name="R3">
<tool name="Generate Template (Bootstrap)" description="Generate a single template" showInMainMenu="false" showInEditor="true" showInProject="true" showInSearchPopup="true" disabled="false
" useConsole="true" showConsoleOnStdOut="false" showConsoleOnStdErr="false" synchronizeAfterRun="true">
<exec>
<option name="COMMAND" value="/bin/bash" />
<option name="PARAMETERS" value="-l $ProjectFileDir$/tools/r3/scripts/runfile-bootstrap.sh $FilePathRelativeToProjectRoot$" />
<option name="WORKING_DIRECTORY" value="$ProjectFileDir$" />
</exec>
</tool>
<tool name="Build All Templates (Bootstrap)" description="Build all template files" showInMainMenu="true" showInEditor="false" showInProject="false" showInSearchPopup="false" disabled="fal
se" useConsole="true" showConsoleOnStdOut="false" showConsoleOnStdErr="false" synchronizeAfterRun="true">
<exec>
<option name="COMMAND" value="/usr/bin/docker exec -it bonsai2 /var/www/bonsai/tools/r3/scripts/bootstrap-run-parallel.sh" />
<option name="PARAMETERS" />
<option name="WORKING_DIRECTORY" value="/usr/bin" />
</exec>
</tool>
<tool name="Setup All Templates (Bootstrap)" description="Setup all templates" showInMainMenu="true" showInEditor="false" showInProject="false" showInSearchPopup="false" disabled="false" u
seConsole="true" showConsoleOnStdOut="false" showConsoleOnStdErr="false" synchronizeAfterRun="true">
<exec>
<option name="COMMAND" value="$ProjectFileDir$/tools/r3/scripts/bootstrap-setup-ramdisc.sh" />
<option name="PARAMETERS" />
<option name="WORKING_DIRECTORY" value="$USER_HOME$/Public/Bonsai/tools/r3/scripts" />
</exec>
</tool>
</toolSet>

For example if i execute the following  in the linux bash shell 

/usr/bin/docker exec -it bonsai2 /var/www/bonsai/tools/r3/scripts/bootstrap-run-parallel.sh

It works just fine

But setup as an internal tool with the path set to /usr/bin

PHPStorm keeps telling me that the program does not exist, even though /usr/bin/docker is defiantly there.