Add Sfold

[reytakop]

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[bgruening]

Please add a .shed.yml to trigger the tests.

[bgruening]

Suggested change

	<param argument="a" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Run clustering on the sampled ensemble?"/>
	<param argument="f" type="data" format="ct" optional="true" label="Constrain data" help="Constraint syntax follows what is used in mfold 3.1"/>
	<param argument="l" type="integer" min="0" optional="true" label="Maximum distance between paired bases"/>
	<param argument="m" type="data" format="ct" optional="true" label="MFE structure" help="If provided, Sfold clustering module will determine the cluster to which this structure belongs."/>
	<param argument="w" type="integer" value="20" label="Length of antisense oligos"/>
	<param argument="i" type="select" label="Module">
	<param argument="-a" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Run clustering on the sampled ensemble?"/>
	<param argument="-f" type="data" format="ct" optional="true" label="Constrain data" help="Constraint syntax follows what is used in mfold 3.1"/>
	<param argument="-l" type="integer" min="0" optional="true" label="Maximum distance between paired bases"/>
	<param argument="-m" type="data" format="ct" optional="true" label="MFE structure" help="If provided, Sfold clustering module will determine the cluster to which this structure belongs."/>
	<param argument="-w" type="integer" value="20" label="Length of antisense oligos"/>
	<param argument="-i" type="select" label="Module">

[reytakop]

I added the .shed.yml file. Thanks.

[reytakop]

The sfold.xml file was edited and completed. I also added a .shed.yml file.

[bgruening]

sh: line 1: /usr/local/bin/gcg2bp.pl: cannot execute: required file not found

[bgruening]

The file is in the container:

root@0c1333b9f6d8:/# find / -name '*gcg2*'
/usr/local/bin/gcg2bp.pl

Shebang looks also good:

root@0c1333b9f6d8:/# head /usr/local/bin/gcg2bp.pl
#!/usr/bin/env perl

#
# Take GCG connect file as input and convert structure
# to base-pair format
#

```

Maybe it was really just the wrong version number.