comparison matchms_convert.xml @ 4:d4609fbf8ca3 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a

3:b9cc12600553

<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
    
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>

        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
    </requirements>

    <command detect_errors='aggressive'><![CDATA[
        python ${matchms_python_cli}
    ]]></command>

<configfiles>
<configfile name="matchms_python_cli">
@init_logger@

from matchms.importing import load_from_msp, load_from_mgf, load_from_json
from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata}))
#if $output_file.output_format == "msp"
save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}")
#else
save_as_${output_file.output_format}(spectra, "${converted_library}")
#end if
</configfile>
</configfiles>

    <inputs>
        <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json"

                    <option value="matchms" selected="true">matchms</option>
                    <option value="massbank">massbank</option>
                    <option value="nist">nist</option>
                    <option value="riken">riken</option>
                    <option value="gnps">gnps</option>
                </param>
            </when>
            <when value="mgf" />
            <when value="json" />
        </conditional>

            <param name="export_peak_comments" value="True"/>
            <param name="output_format" value="msp"/>
            <param name="export_style" value="matchms"/>
            <output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
        </test>
    </tests>


    <help><![CDATA[
        Description

4:d4609fbf8ca3

<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy2" profile="21.05">
    <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
    
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>

        <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
    </requirements>

    <command detect_errors='aggressive'><![CDATA[
        python ${matchms_python_cli}
        #if $output_file.output_format == "msp":
        #if $output_file.export_style == "ms_lima":
        &&
        sh ${ms_lima_output}
        #end if
        #end if
    ]]></command>

<configfiles>
<configfile name="matchms_python_cli">
@init_logger@

from matchms.importing import load_from_msp, load_from_mgf, load_from_json
from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata}))
#if $output_file.output_format == "msp"
#if $output_file.export_style == "ms_lima"
save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "riken")
#else
save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}")
#end if
#else
save_as_${output_file.output_format}(spectra, "${converted_library}")
#end if
</configfile>
<configfile name="ms_lima_output">
sed -E "s,[[:space:]]+, ,g" ${converted_library} > ${converted_library}.tmp

grep -rl 'IONMODE' . | xargs sed '/IONMODE/d' ${converted_library}.tmp > ${converted_library}.tmp1
grep -rl 'CHARGE' . | xargs sed '/CHARGE/d' ${converted_library}.tmp1 > ${converted_library}.tmp2
grep -rl 'COMPOUND_NAME' . | xargs sed 's/COMPOUND_NAME/NAME/g' ${converted_library}.tmp2 > ${converted_library}.tmp3

mv ${converted_library}.tmp3 ${converted_library}
rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp3 ${converted_library}.tmp
</configfile>
</configfiles>

    <inputs>
        <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json"

                    <option value="matchms" selected="true">matchms</option>
                    <option value="massbank">massbank</option>
                    <option value="nist">nist</option>
                    <option value="riken">riken</option>
                    <option value="gnps">gnps</option>
                    <option value="ms_lima">ms-lima</option>
                </param>
            </when>
            <when value="mgf" />
            <when value="json" />
        </conditional>

            <param name="export_peak_comments" value="True"/>
            <param name="output_format" value="msp"/>
            <param name="export_style" value="matchms"/>
            <output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
        </test>
        <test>
            <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
            <param name="harmonization_metadata" value="True"/>
            <param name="export_peak_comments" value="False"/>
            <param name="output_format" value="msp"/>
            <param name="export_style" value="ms_lima"/>
            <output name="converted_library" file="convert/ms_lima_output.msp" ftype="msp"/>
        </test>
    </tests>


    <help><![CDATA[
        Description