view macros.xml @ 1:724dcbb35c9a draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/blob/main/tools/saqc/ commit b674325a07b6e964e25cd65967149018dc2671fe

<macros>
<xml name="requirements">
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">saqc</requirement>
    </requirements>
</xml>

<token name="@TOOL_VERSION@">2.6.0</token>
<token name="@VERSION_SUFFIX@">0</token>

<xml name="citations">
    <citations>
        <citation type="doi">https://doi.org/10.1016/j.envsoft.2023.105809</citation>
    </citations>
</xml>

<xml name="field">
    <param argument="field"
           label="Field"
           optional="false"
           value=""
           type="text"
           help="Variable to process"/>
</xml>

<xml name="field_multiple">
    <repeat name="field_repeat" title="field(s)" min="1">
        <param argument="field"
               label="Field"
               optional="false"
               value=""
               type="text"
               help="Variable to process"/>
    </repeat>
</xml>

<xml name="flag">
    <param argument="flag"
           label="Flag"
           optional="true"
           value="255.0"
           type="float"
           help="The flag value the function uses to mark observations"/>
</xml>

<xml name="saqc_tests">
    <tests>
    <expand macro="config_tests"/>
    <test>
        <param name="data" value="test1/data.csv" ftype="csv"/>
        <repeat name="methods_repeat">
            <conditional name="module_cond">
                <param name="module_select" value="outliers"/>
                <conditional name="method_cond">
                    <param name="method_select" value="flagRange"/>
                    <param name="field" value="SM2"/>
                    <param name="max" value="60.0"/>
                    <param name="min" value="10.0"/>
                    
                    <param name="flag" value="255.0"/>
                </conditional>
            </conditional>
        </repeat>
        <repeat name="methods_repeat">
            <conditional name="module_cond">
                <param name="module_select" value="outliers"/>
                <conditional name="method_cond">
                
                    <param name="method_select" value="flagZScore"/>

                    <repeat name="field_repeat">
                    <param name="field" value="SM2"/>
                    </repeat>
                    <param name="center" value="false"/>
                    <conditional name="window_cond">
                        <param name="window_select_type" value="timedelta"/>
                        <param name="window" value="30d"/>
                    </conditional>
                    <param name="thresh" value="3.5"/>
                    <param name="method" value="modified"/>
                    
                    <param name="flag" value="255.0"/>
                </conditional>
            </conditional> 
        </repeat>
        <repeat name="methods_repeat">
            <conditional name="module_cond">
                <param name="module_select" value="tools"/>
                <conditional name="method_cond">
                    <param name="method_select" value="plot"/>
                    <param name="field" value="SM2"/>
                    <param name="path" value="test"/>
                    <conditional name="history_cond">
                        <param name="history_select_type" value="valid" />
                        <param name="history" value="valid" />
                    </conditional>
                    <param name="mode" value="oneplot"/>
                    <param name="max_gap" value="" />
                    <param name="xscope" value="" />
                    <param name="yscope" value="" />
                    <param name="dfilter" value="inf" />
                </conditional>
            </conditional>
        </repeat>

        <output name="output" value="test1/out.csv" ftype="csv"/>
        <output name="config_out" ftype="txt">
            <assert_contents>
                <has_n_lines n="4"/>
                <has_n_columns n="2" sep=";"/>
                <has_text_matching expression="flagRange.*max=60.0.*min=10.0"/>
                <has_text_matching expression='flagZScore.*method="modified".*thresh=3.5.*window="30d"'/>
                <has_text_matching expression='plot.*dfilter=float\(&apos;inf&apos;\).*history="valid".*path="test"'/>
            </assert_contents>
        </output>
            
        <output_collection name="plots" type="list">
            <element name="test" ftype="png">
                <assert_contents>
                    <has_text text="PNG"/>
                    <has_size value="120k" delta="10k"/>
                </assert_contents>
            </element>
        </output_collection>
    </test>
    </tests>
</xml>
</macros>