annotate alchemical_analysis/alchemical_analysis.xml @ 1:c1fa72716efc draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit eefe89bfcd6c3e98f4e774e508ad0659dcc2f65c"

<tool id="alchemical_analysis" name="Alchemical Analysis" version="1.0.2">
    <description>Analysis of alchemical free energy calculations</description> 
    <requirements>
         <requirement type="package" version="1.0.2">alchemical-analysis</requirement>
         <requirement type="package" version="3.0.3">pymbar</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       ln -s '$datain' ./data.tar &&
       tar xf ./data.tar && 
       mkdir ./RESULTS/ &&
            #if $skiplambda == "":
                alchemical_analysis -d data -o ./RESULTS -t '$temp' -s '$time' -c -q xvg -p '$prefix' -g -e -f 10 -w -u '$units' &>> '$output'
            #else: 
                 alchemical_analysis -d data -o ./RESULTS -t '$temp' -s '$time' -k '$skiplambda' -c -q xvg -p '$prefix' -g -e -f 10 -w -u '$units' &>> '$output'
            #end if
    ]]></command>
    <inputs>
    <param format="tar" name="datain" type="data" label="TI/FEP data output"/>
    <param name="prefix" type="text" value="md" label="Prefix for datafile sets" help="This should be md if you used the alchemical simulator tool"/>
    <param name="temp" type="integer" value="300" label="Temperature (K)"/>
    <param name="time" type="integer" value="0" label="Equilibration time (ps)" help="Discard data prior to this specified time as 'equilibration' data." />
    <param name="units" type="select" label="Units to report energies" >
        <option value="kcal">kcal</option>
        <option value="kJ">kJ</option>
        <option value="kBT">kT</option>
    </param>
    <param name="skiplambda" type="text" label="Indices of lambda states to skip" help="Give a string of lambda indices separated by '-' (e.g. 2-3) and they will be removed from the analysis.  Default: will use all the windows.">
        <validator type="regex" message="Only numeric values and '-' allowed">^[0-9-]*$</validator>
    </param>
    </inputs>
    <outputs>
        <data name="output" format="txt" label="output">
        </data>
        <data name="results" format="txt" from_work_dir="./RESULTS/results.txt" label="Results"/>
        <data name="change" format="txt" from_work_dir="./RESULTS/dF_t.txt" label="Free energy change dF(t)"/>
        <data name="convergence" format="png" from_work_dir="./RESULTS/dF_t.png" label="Convergence Plot dF(t)"/>
        <data name="overlap" format="png" from_work_dir="./RESULTS/O_MBAR.png" label="Overlap Matrix"/>
        <data name="cfm" format="png" from_work_dir="./RESULTS/cfm.png" label="Curve Fitting Method (CFM) based consistency inspector"/>
        <data name="df_state" format="png" from_work_dir="./RESULTS/dF_state_long.png" label="Free energy change breakdown"/>
        <data name="ti_plot" format="png" from_work_dir="./RESULTS/dhdl_TI.png" label="Thermodynamic Integration plot"/>
    </outputs>
    <tests>
         <test>
            <param name="datain" value="data.tar" ftype="tar"/>
            <param name="prefix" value="md"/>
            <param name="temp" value="300"/>
            <param name="time" value="0"/>
            <param name="units" value="kcal"/>
            <param name="lambda" value="no"/>
            <output name="change" file="Free_energy_change_dF(t).txt" />
        </test>
    </tests>  
    <help><![CDATA[   
.. class:: infomark
 
**What it does**
        

This tool can run analysis of alchemical free energy simulations.

_____


.. class:: infomark

**Input**

       - TAR archive file of the GROMACS XVG files from free energy simulations. Note that simulations should be at least 100 ps in length.

_____

       
.. class:: infomark

**Output**

       - Report and free energy outputs.
       - Overlap matrix of free energy windows (as PNG).
       - Convergence plot (as PNG).
       - Curve Fitting Method (CFM) based consistency inspector (as PNG).
       - Free energy change breakdown (as PNG).
       - Thermodynamic Integration plot (as PNG).

    ]]></help>
    <citations>
      <citation type="doi">10.1007/s10822-015-9840-9</citation>
    </citations>
</tool>