annotate qcxms_getres.xml @ 3:89b026d67e9f draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 5a088c3d758c9a1dbd119dad55ecffa173139a40

<tool id="qcxms_getres" name="QCxMS get results" version="@TOOL_VERSION@+galaxy2" profile="22.09">
    <description>Get result of the Production run to obtain a QCxMS simulated mass spectrum</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam"/>
    <expand macro="creator"/>
    <expand macro="requirements"/>

    <command detect_errors="exit_code"><![CDATA[
        python3 '${get_res}' &&
        /plotms_bin/PlotMS.v.6.2.0/plotms &&
        sh ${__tool_directory__}/msp_out.sh
    ]]></command>

    <configfiles>
        <configfile name="get_res">
#set res_collection = str("', '").join([str($f) for $f in $res_files])

with open('$mol', 'r') as file:
    lines = file.readlines()
    molname = lines[1]

with open('molname.txt', 'w') as file:
    file.write(molname)

input_files = '$res_collection'
output_file = 'tmpqcxms.res'

with open(output_file, 'w') as output:
    for file_path in input_files:
        with open(file_path, 'r') as input_file:
            output.write(input_file.read())

        </configfile>
    </configfiles>

    <inputs>
        <param type="data" name="mol" label="Molecule 3D structure [.xyz]" format="xyz" />
        <param type="data_collection" collection_type="list" name="res_files" label="res files [.res]" format="txt,text"/>
    </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}"/>
    </outputs>

    <tests>
        <test>
            <param name="mol" value="mol.xyz" ftype="xyz"/>
            <param name="res_files">
                <collection type="list">
                  <element name="res_files_1" value="res_files/TMP.1_qcxms.txt" />
                  <element name="res_files_2" value="res_files/TMP.2_qcxms.txt" />
                  <element name="res_files_3" value="res_files/TMP.3_qcxms.txt" />
                </collection>
            </param>
            <output name="msp_output" file="output.msp" ftype="msp"/>
        </test>
    </tests>

    <help><![CDATA[
        The QCxMS getres tool is used to simulate mass spectra for a given molecule. 
        This tool take res and molecules files and generates simulated mass spectra.
        ]]>
    </help>

    <citations>
        <citation type="doi">10.1002/anie.201300158</citation>
        <citation type="doi">10.1039/C4OB01668H</citation>
        <citation type="doi">10.1021/jp5096618</citation>
        <citation type="doi">10.1255/ejms.1313</citation>
        <citation type="doi">10.1021/acs.jpca.6b02907</citation>
    </citations>
</tool>