Added XML for ASRP PDF refinement tool using DiffPy-CMI
Work includes:
My testing:
- Using our NDIP galaxy repo, I cloned it locally into a
galaxy
directory for the project - I used this repo and my branch to create
galaxy-tools
- In
galaxy
directory, I copiedconfig/tool_conf.xml.sample
toconfig/tool_conf.xml
- I added the following section to the
config/tool_conf.xml
:
<section id="neutrons_asrp" name="Automated Structural Refinement">
<tool file="../../galaxy-tools/tools/neutrons/asrp_single_peak_fitting.xml"/>
<tool file="../../galaxy-tools/tools/neutrons/asrp_pattern_matching.xml"/>
<tool file="../../galaxy-tools/tools/neutrons/asrp_gsas2_refinement.xml"/>
<tool file="../../galaxy-tools/tools/neutrons/asrp_diffpy_cmi_refinement.xml"/>
</section>
NOTE: the relative path was with galaxy
and galaxy-tools
at the same level; the tool config file is in galaxy/config
so ../../galaxy-tools
is correct for that setup.
- I then ran
sh run.sh
in thegalaxy
to start up my local galaxy instance with the new tool - I uploaded the test data from this project as datasets in galaxy instance: https://code.ornl.gov/neutrons/asrp/ndip-tool-containers/-/tree/main/asrp/diffpy_cmi_refinement/tests/data
- CIF filename:
si.cif
- PDF filename:
NOM_9999_Si_d_new_NewCapA_ftfrgr.gr
- CIF filename:
- I ran the tool successfully with the correctly outputted files: