Commit 6be9c849 authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

remove galaxy config from tool sources

parent 455c39c0

galaxy/tool_conf.xml

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<?xml version='1.0' encoding='utf-8'?>

<toolbox monitor="true">

  <label id="neutrons" text="Neutrons" version="" />

    <section id="neutrons_getext" name="Get Data">

      <tool file="neutrons/import_oncat.xml" />

      <tool file="data_source/upload.xml" />

      <tool hidden="true" file="neutrons/register.xml" />

      <tool file="neutrons/ingress.xml" />

    </section>



    <section id="neutrons_tests" name="Neutrons Test Tools">

      <tool file="neutrons/remote_command.xml"/>

      <tool file="neutrons/file_head.xml"/>

      <tool file="neutrons/fractal.xml"/>

      <tool file="neutrons/monitor.xml" />

    </section>

    

    <section id="neutrons_asrp" name="Automated Structural Refinement">

      <tool file="neutrons/asrp_single_peak_fitting.xml"/>

      <tool file="neutrons/asrp_pattern_matching.xml"/>

      <tool file="neutrons/asrp_gsas2_refinement.xml"/>

      <tool file="neutrons/asrp_diffpy_cmi_refinement.xml"/>

    </section>

    

    <section id="neutrons_ins" name="Inelastic Neutron Scattering">

      <tool file="neutrons/qclimax.xml"/>

      <tool file="neutrons/qclimaxIni.xml"/>

    </section>

    

    <section id="neutrons_dca" name="Advanced Neutron Data Analysis for Quantum Materials">

      <tool file="neutrons/dca_convergence.xml" />

      <tool file="neutrons/dca_binning.xml" />

      <tool file="neutrons/dca_s_of_q_omega.xml" />

      <tool file="neutrons/dca_analysis_to_maxent.xml" />

      <tool file="neutrons/dca_maxent.xml" />

      <tool file="neutrons/dca_maxent_plot.xml" />

      <tool file="neutrons/rpa_mrpapp.xml" />

      <tool file="neutrons/rpa_plot_chirpa.xml" />

    </section>

    

    <section id="neutrons_mcu" name="Monte Carlo Ray Tracing">

      <tool file="neutrons/mcu_get_instrument.xml" />

      <tool file="neutrons/mcu_incident_beamline_configurator.xml" />

      <tool file="neutrons/mcu_incident_beamline_simulator.xml" />

      <tool file="neutrons/mcu_mcpl_tool.xml" />

      <tool file="neutrons/interactivetool_reduce120.xml" />

      <tool file="neutrons/mcu_sample_simulator.xml" />

    </section>

    

    <section id="ndip_datared" name="Data Reduction">

      <tool file="neutrons/usans.xml"/>

      <tool file="neutrons/gpsans.xml"/>

      <tool file="neutrons/topaz_reduce.xml"/>

      <tool file="neutrons/topaz_combine.xml"/>

    </section>

    

    <section id="ndip_amml" name="Atomistic modeling and machine learning">

      <tool file="neutrons/amml_cp2k.xml"/>

      <tool file="neutrons/amml_cp2k_convert.xml"/>

      <tool file="neutrons/amml_train.xml"/>

      <tool file="neutrons/amml_lammps.xml"/>

      <tool file="neutrons/amml_oclimax.xml"/>

      <tool file="neutrons/amml_pclimax.xml"/>

    </section>

    

    <section id="neutrons_interactivetools" name="Interactive Tools">

      <tool file="neutrons/interactivetool_generic_output.xml" />

      <tool file="neutrons/ct_reconstruction.xml" />

      <tool file="neutrons/interactivetool_paraview.xml" />

    </section>

    

    <section id="neutrons_amira" name= "Amira Visualization">

      <tool file="neutrons/interactivetool_thinlinc.xml" />

    </section>

    

    <section id="neutrons_misc" name="Miscellaneous">

      <tool file="neutrons/get_experiment_location.xml" />

    </section>

      

    <section id="ndip_mlsans" name="MLSANS">

	  <tool file="neutrons/mlsans_fit_Yukawa_sq.xml" />

    </section>





  <label id="generic" text="Generic" version="" />



  <section id="send" name="Send Data">

    <tool file="data_export/send.xml" />

    <tool file="data_export/export_remote.xml" />

    <tool file="neutrons/export.xml"  />

  </section>



  <section id="collection_operations" name="Collection Operations">

    <tool file="${model_tools_path}/unzip_collection.xml" />

    <tool file="${model_tools_path}/zip_collection.xml" />

    <tool file="${model_tools_path}/filter_failed_collection.xml" />

    <tool file="${model_tools_path}/filter_empty_collection.xml" />

    <tool file="${model_tools_path}/flatten_collection.xml" />

    <tool file="${model_tools_path}/merge_collection.xml" />

    <tool file="${model_tools_path}/relabel_from_file.xml" />

    <tool file="${model_tools_path}/filter_from_file.xml" />

    <tool file="${model_tools_path}/sort_collection_list.xml" />

    <tool file="${model_tools_path}/tag_collection_from_file.xml" />

    <tool file="${model_tools_path}/apply_rules.xml" />

    <tool file="${model_tools_path}/build_list.xml" />

    <tool file="${model_tools_path}/build_list_1.2.0.xml" />

    <tool file="${model_tools_path}/extract_dataset.xml" />

  </section>



  <section id="expression_tools" name="Expression Tools">

    <tool file="expression_tools/parse_values_from_file.xml"/>

  </section>



  <section id="textutil" name="Text Manipulation">

    <tool file="filters/fixedValueColumn.xml" />

    <tool file="filters/catWrapper.xml" />

    <tool file="filters/cutWrapper.xml" />

    <tool file="filters/mergeCols.xml" />

    <tool file="filters/convert_characters.xml" />

    <tool file="filters/CreateInterval.xml" />

    <tool file="filters/cutWrapper.xml" />

    <tool file="filters/changeCase.xml" />

    <tool file="filters/pasteWrapper.xml" />

    <tool file="filters/remove_beginning.xml" />

    <tool file="filters/randomlines.xml" />

    <tool file="filters/headWrapper.xml" />

    <tool file="filters/tailWrapper.xml" />

    <tool file="filters/trimmer.xml" />

    <tool file="filters/wc_gnu.xml" />

    <tool file="filters/secure_hash_message_digest.xml" />

  </section>



  <section id="filter" name="Filter and Sort">

    <tool file="stats/filtering.xml" />

    <tool file="filters/sorter.xml" />

    <tool file="filters/grep.xml" />

    <tool file="filters/grep_1.0.1.xml"/>

  </section>



  <section id="group" name="Join, Subtract and Group">

    <tool file="filters/joiner.xml" />

    <tool file="filters/compare.xml" />

    <tool file="stats/grouping.xml" />

  </section>



  <section id="stats" name="Statistics">

    <tool file="stats/gsummary.xml" />

    <tool file="filters/uniq.xml" />

  </section>



</toolbox>

galaxy/tools/neutrons/mlsans_fit_yukawa_sq.xml

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Original line number Diff line number Diff line 
 <tool id="neutrons_mlsans_fit_yukawa_sq" name="fit_Yukawa_IQ"  profile="22.04" version="0.1.5-dev3">

  <description></description>

    <creator>

        <person name="ML-SANS Tools"/>

        <organization url="https://www.ornl.gov/" name="ORNL"/>

    </creator>

    <requirements>

        <container type="docker">savannah.ornl.gov/ndip/tool-sources/ml-assisted-sans-data-analysis/fit_yukawa_sq@sha256:9adfe752a9859aa252216bfba8a57af4235c983bc7fcfb6f1c92425123b7bbe0</container>

    </requirements>

    <command detect_errors="exit_code"><![CDATA[

        python3 /src/curvefit.py -i $input $C $I_inc $sigma $d_sigma $phi $kappa $A || echo python finished && mv output.png $output && cp output.txt $output2

    ]]></command>

    <inputs>

        <param name="input" type="data" optional="false" label="ASCII data"/>

        <param name="C" type="text" value="4000 3500 4500" label="C" optional="false" help="Contrast"/>

        <param name="I_inc" type="text" value="0.5 0.1 2" label="I_inc" optional="false" help="Incoherent background"/>

        <param name="sigma" type="text" value="1 0.9 1.1" label="σ" optional="false" help="Particle diameter"/>

        <param name="d_sigma" type="text" value="0.07 0.02 0.1" label="d_σ" optional="false" help="Particle size polydispersity"/>

        <param name="phi" type="text" value="0.1 0.05 0.25" label="Φ" optional="false" help="Volume fraction"/>

        <param name="kappa" type="text" value="0.2 0.1 0.3" label="1/κD" optional="false" help="Screening constant"/>

        <param name="A" type="text" value="10 1 20" label="βA" optional="false" help="Repulsion strength"/>

    </inputs>

	

    <outputs>

        <data name="output" format="png" label="fitting results plot">

        </data>

        <data name="output2" format="txt" label="fitting results">

        </data>

    </outputs>

    <help><![CDATA[

        **What it does**

        

        Fit the input hard sphere Yukawa colloid I(Q) curve. 



        **Usage**



        Initial guess, lower bound and upper bound are separated using spaces. 

        Q points are rescaled such that QD in 0.2:0.2:16, the sigma fitting parameter reflects the differences between the actual particle radius and the initial guesses.



        **Acknowledgement**

        

        This research was sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U. S. Department of Energy.

]]></help>

    <citations>

    <!-- Example of annotating a citation using a DOI. -->

        <citation type="doi">10.1038/s42005-021-00778-y</citation>

        <citation type="doi">10.1016/j.cartre.2023.100252</citation>

        <citation type="doi">10.1107/S1600576724004515</citation>

    </citations>

    <tests>

        <test>

            <param name="input" value="example_IQ_Yukawa.csv" />

            <param name="C"  value="4000 3500 4500" />

            <param name="I_inc"  value="0.5 0.1 2" />

            <param name="sigma"  value="1 0.9 1.1" />

            <param name="d_sigma"  value="0.07 0.02 0.1" />

            <param name="phi"  value="0.1 0.05 0.25" />

            <param name="kappa"  value="0.2 0.1 0.3" />

            <param name="A" value="10 1 20" />

        </test>

    </tests>

</tool>

galaxy/tools/neutrons/test-data/example_IQ_Yukawa.csv

deleted100644 → 0
+0 −100
Original line number Diff line number Diff line 
0.2,876.1466294070176

0.4,867.5849984656128

0.6000000000000001,881.9455162178297

0.8,918.2373157065572

1.0,1003.7320672948202

1.2000000000000002,1065.0522949308408

1.4000000000000001,1114.9882125107242

1.6,1166.8626196048185

1.8,1224.962503518862

2.0,1300.910646289847

2.2,1384.2670669620718

2.4000000000000004,1468.4915281965366

2.6,1552.8272608062778

2.8000000000000003,1650.0438485623595

3.0,1761.3088058620938

3.2,1874.923395036646

3.4000000000000004,1961.5968775147228

3.6,2004.3107783877801

3.8000000000000003,1993.2557087923078

4.0,1933.9983787258498

4.2,1824.2850724971884

4.4,1672.4439400076371

4.6000000000000005,1503.0064312661168

4.800000000000001,1325.431552316714

5.0,1150.5961474451494

5.2,984.4454402048426

5.4,830.2129312137488

5.6000000000000005,691.8389998280635

5.800000000000001,577.2195949752779

6.0,482.8311798173546

6.2,403.23507944716954

6.4,334.4699329296535

6.6000000000000005,274.2191135571878

6.800000000000001,220.75411979977912

7.0,175.75735847585332

7.2,138.1872197849548

7.4,106.89011201574877

7.6000000000000005,81.44402161159825

7.800000000000001,60.81907529344448

8.0,44.187108773755824

8.200000000000001,31.295162982856297

8.4,21.63043973815487

8.6,14.927273927701803

8.8,10.765319017231104

9.0,8.68728187807691

9.200000000000001,8.229730209876085

9.4,8.995523642236654

9.600000000000001,10.599702046249716

9.8,12.750907894847236

10.0,15.173801290554321

10.200000000000001,17.67118894200872

10.4,20.07505924353969

10.600000000000001,22.215319220327856

10.8,23.96084112049982

11.0,25.275038922161592

11.200000000000001,26.12779205416269

11.4,26.50010474197904

11.600000000000001,26.488954458615176

11.8,26.10850037496191

12.0,25.36352363536224

12.200000000000001,24.261878167938143

12.4,22.866555808387215

12.600000000000001,21.25659971034301

12.8,19.506773635624043

13.0,17.69314217779777

13.200000000000001,15.828306581337898

13.4,13.974096886071838

13.600000000000001,12.175138285020292

13.8,10.490454123460916

14.0,8.93187302963528

14.200000000000001,7.539153662674271

14.4,6.3197034798233975

14.600000000000001,5.290041371719787

14.8,4.4501551748229655

15.0,3.7942105639704575

15.200000000000001,3.312165850728488

15.4,2.984648382430284

15.600000000000001,2.7945456730064855

15.8,2.7216573295633646

16.0,2.7480499871030997

16.2,2.8517082151714197

16.400000000000002,3.0135632589476025

16.6,3.210363252191553

16.8,3.4215768922314664

17.0,3.632531363358618

17.2,3.8309528727747457

17.400000000000002,4.000577957801227

17.6,4.135928150444569

17.8,4.234334576407528

18.0,4.292978020750253

18.2,4.308497667294391

18.400000000000002,4.27868494459527

18.6,4.196538014390359

18.8,4.074269300135645

19.0,3.9199483979402894

19.200000000000003,3.7437341869587684

19.400000000000002,3.5443471913676774

19.6,3.3261631384694184

19.8,3.098574194054552

20.0,2.8685100320903745