comparison qcxms_prod_run.xml @ 2:b566b27247f7 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 4018b84dd3c735d16f488094f001a19e634fe1a2

1:bc099c440016

<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy1" profile="21.05">
    <description>Production run to obtain a QCxMS simulated mass spectrum</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="creator"/>
    <expand macro="requirements"/>

    <command detect_errors="exit_code"><![CDATA[
        python3 '${create_folder_structure}' &&
        find TMPQCXMS/*/ -type d | xargs -I {} -P \${GALAXY_SLOTS:-1} sh -c 'cd {} && /qcxms_bin/qcxms --prod >> $log' &&
        /qcxms_bin/getres &&
        /plotms_bin/PlotMS.v.6.2.0/plotms &&
        sh ${__tool_directory__}/msp_out.sh
    ]]></command>

    <environment_variables>
        <environment_variable name="OMP_NUM_THREADS">1,2,1</environment_variable>
    </environment_variables>

    <configfiles>
        <configfile name="create_folder_structure">
import os
import shutil

#set in_collection = str("', '").join([str($f) for $f in $in_files])
#set start_collection = str("', '").join([str($f) for $f in $start_files])
#set xyz_collection = str("', '").join([str($f) for $f in $xyz_files])

#set names = str("', '").join([str($f.name) for $f in $xyz_files])
names = '$names'
folder_names = [x.split("_")[0] for x in names]

in_collection = '$in_collection'
start_collection = '$start_collection'
xyz_collection = '$xyz_collection'

# Create a new output folder to store the result
output_path = 'TMPQCXMS'
os.makedirs(output_path, exist_ok=True)

for folder_name, in_file, start_file, xyz_file in zip(folder_names, in_collection, start_collection, xyz_collection):
    new_folder_path = os.path.join(output_path, folder_name)
    os.makedirs(new_folder_path, exist_ok=True)

    shutil.copy2(os.path.join(os.path.dirname(in_collection[0]), in_file), os.path.join(new_folder_path, 'qcxms.in'))
    shutil.copy2(os.path.join(os.path.dirname(start_collection[0]), start_file), os.path.join(new_folder_path, 'qcxms.start'))
    shutil.copy2(os.path.join(os.path.dirname(xyz_collection[0]), xyz_file), os.path.join(new_folder_path, 'start.xyz'))

        </configfile>
    </configfiles>

    <inputs>
        <param type="data_collection" collection_type="list" name="in_files" label="in files [.in]" format="in,txt,text"/>
        <param type="data_collection" collection_type="list" name="start_files" label="start files [.start]" format="start,txt,text"/>
        <param type="data_collection" collection_type="list" name="xyz_files" label="xyz files [.xyz]" format="xyz,txt,text"/>
        <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs" help="Output the logfile."/>
    </inputs>

    <outputs>
        <data name="msp_output" format="msp" from_work_dir="simulated_spectra.msp" label="simulated_spectra.msp generated by ${tool.name} on ${on_string}"/>
        <data name="log" format="txt" label="logfile of ${tool.name} on ${on_string}">
            <filter>store_extended_output</filter>
        </data>
    </outputs>

    <tests>
        <test expect_failure="true"/>
    </tests>

    <help><![CDATA[
        The QCxMS production run tool is used to simulate mass spectra for a given molecule using the QCxMS (Quantum Chemistry by Mass Spectrometry) method. 
        This tool generates simulated mass spectra based on the equilibrium structure of a molecule and allows you to perform QCxMS production runs.
        For detail information visit the documentation at https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms_run.html#excecuting-the-production-runs
        ]]>
    </help>

    <citations>

2:b566b27247f7

<tool id="qcxms_production_run" name="QCxMS production run" version="@TOOL_VERSION@+galaxy2" profile="22.09">
    <description>Production run to obtain a QCxMS simulated mass spectrum</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="creator"/>
    <expand macro="requirements"/>

    <command detect_errors="exit_code"><![CDATA[
        python3 '${create_folder_structure}' &&
        (cd TMPQCXMS/*/ && /qcxms_bin/qcxms --prod) >> $log
    ]]></command>

    <environment_variables>
        <environment_variable name="OMP_NUM_THREADS">1,2,1</environment_variable>
    </environment_variables>

    <configfiles>
        <configfile name="create_folder_structure">
import os
import shutil

names = '$xyz_file.name'
folder_name = names.split("_")[0]


# Create a new output folder to store the result
output_path = 'TMPQCXMS'
os.makedirs(output_path, exist_ok=True)

new_folder_path = os.path.join(output_path, folder_name)
os.makedirs(new_folder_path, exist_ok=True)

shutil.copy2(os.path.join(os.path.dirname('$in_file'), '$in_file'), os.path.join(new_folder_path, 'qcxms.in'))
shutil.copy2(os.path.join(os.path.dirname('$start_file'), '$start_file'), os.path.join(new_folder_path, 'qcxms.start'))
shutil.copy2(os.path.join(os.path.dirname('$xyz_file'), '$xyz_file'), os.path.join(new_folder_path, 'start.xyz'))

        </configfile>
    </configfiles>

    <inputs>
        <param type="data" name="in_file" label="in files [.in]" format="txt,text"/>
        <param type="data" name="start_file" label="start files [.start]" format="txt,text"/>
        <param type="data" name="xyz_file" label="xyz files [.xyz]" format="xyz,txt,text"/>
        <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs" help="Output the logfile."/>
    </inputs>

    <outputs>
        <data name="log" format="txt" label="logfile_of_${tool.id}_on_${on_string}">
            <filter>store_extended_output</filter>
        </data>
        <data name="res_files" format="txt" from_work_dir="TMPQCXMS/*/qcxms.res" label="res files generated by ${tool.name} on ${on_string}"/>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="in_file" value="TMP.1_qcxms_in.txt" ftype="txt"/>
            <param name="start_file" value="TMP.1_qcxms_start.txt" ftype="txt"/>
            <param name="xyz_file" value="TMP.1_start_xyz.txt" ftype="txt"/>
            <output name="res_files" file="res_out.txt" ftype="txt"/>
        </test>
    </tests>

    <help><![CDATA[
        The QCxMS production run tool is used to simulate mass spectra for a given molecule using the QCxMS (Quantum Chemistry by Mass Spectrometry) method. 
        This tool allows you to perform QCxMS production runs and generates res files which are further used by QCxMS get results tool to produce the simulated mass spectra.
        For detail information visit the documentation at https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms_run.html#excecuting-the-production-runs
        ]]>
    </help>

    <citations>