comparison msmetaenhancer.xml @ 3:f387ebd6b734 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 6858f7bc3c3cf68fd5002a2241c79923b2ca9acd"

2:8338640d8676

<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy1">
    <description>annotate MS data</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <configfiles>
        <configfile name="msmetaenhancer_python_cli">
            python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
            --input_file "$input_file" \
            --output_file "$output_file" \
            #if $options.output_log:
            --log_file "$log_file"\
            #end if
            #if len($ordered_jobs) != 0:
                #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
            #else:
                #set ordered_jobs = ""

        <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
            <expand macro="job_options" />
        </param>

        <section name="options" title="Options">
            <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE"
                   checked="false" help="Preserve a log with details about the annotation process."/>
        </section>
    </inputs>

    <outputs>
        <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
        <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
           <filter>options['output_log']</filter>
       </data>
    </outputs>

    <tests>
        <test>

3:f387ebd6b734

<tool id="msmetaenhancer" name="MSMetaEnhancer" version="@TOOL_VERSION@+galaxy0">
    <description>annotate MS data</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <configfiles>
        <configfile name="msmetaenhancer_python_cli">
            python3 ${__tool_directory__}/msmetaenhancer_wrapper.py \
            --input_file "$input_file" \
            --output_file "$output_file" \
            #if $options.logging.output_log:
            --log_file "$log_file" \
            --log_level "$options.logging.log_level" \
            #end if
            #if len($ordered_jobs) != 0:
                #set ordered_jobs = ",".join([str($job.ordered_jobs_select) for $job in $ordered_jobs]) + ","
            #else:
                #set ordered_jobs = ""

        <param name="jobs" type="select" label="Other conversions" multiple="true" optional="true">
            <expand macro="job_options" />
        </param>

        <section name="options" title="Options">
            <conditional name="logging">
                <param label="Save the log file" name="output_log" type="boolean" truevalue="TRUE" falsevalue="FALSE"
                       checked="false" help="Preserve a log with details about the annotation process."/>
                <when value="TRUE">
                    <param name="log_level" type="select" label="Log level"
                           help="Severity of log messages  present in the log file.">
                        <option value="error">ERROR</option>
                        <option value="warning">WARNING</option>
                        <option value="info" selected="true">INFO</option>
                    </param>
                </when>
            </conditional>
        </section>
    </inputs>

    <outputs>
        <data label="MSMetaEnhancer on ${on_string}" name="output_file" format="msp" />
        <data label="Log of MSMetaEnhancer on ${on_string}" name="log_file" format="txt">
           <filter>options['logging']['output_log']</filter>
       </data>
    </outputs>

    <tests>
        <test>