comparison w4mcorcov.xml @ 10:9a52306991b3 draft

planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552

9:06c51af11531

<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.13">
    <description>OPLS-DA Contrasts of Univariate Results</description>
    <macros>
        <xml name="paramPairSigFeatOnly">
            <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
                label="Retain only pairwise-significant features"

            help="sample metadata, one row per sample" />
        <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)"
            type="data" help="variable metadata, one row per variable" />
        <param name="facC" type="text"
            label="Factor of interest"
            help="REQUIRED - The name of the column of sampleMetadata corresponding to the qualitative variable used to define the contrasts.  Except when the 'Univariate Significance-test' is set to 'none', this also must be a portion of the column names in the variableMetadata file."/>
        <conditional name="signif_test">
            <param name="tesC" label="Univariate significance-test" type="select" help="Either 'none' or the name of the statistical test that was run by the 'Univariate' tool to produce the variableMetadata file; that name must also be a portion of the column names in that file.">
                <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
                <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
                <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>

                    <add value="&#63;"  /> <!-- ? what, question mark -->
                    <add value="&#91;"  /> <!-- [ l-squib, left-squre-bracket -->
                    <add value="&#92;"  /> <!-- \ whack, backslash -->
                    <add value="&#93;"  /> <!-- ] r-squib, right-squre-bracket -->
                    <add value="&#94;"  /> <!-- ^ hat, caret -->
                    <add value="&#123;" /> <!-- { l-cube, left-curly-bracket -->
                    <add value="&#124;" /> <!-- | pipe -->
                    <add value="&#125;" /> <!-- } r-cube, right-curly-bracket -->
                    <!-- IMPORTANT - Note that single and double quotes are not part of this list; they have the potential to make the 'command' section insecure or broken. -->
                </valid>
            </sanitizer>
        </param>
        <param name="matchingC" label="Level-name matching" type="select" help="How to specify level-names generically. (See help below for details on using wild cards or regular expressions.)">
            <option value="none">do no generic matching (default)</option>
            <option value="wildcard" selected="true">use wild-cards for matching level-names</option>
            <option value="regex">use regular expressions for matching level-names</option>
        </param>
        <param name="labelFeatures" type="text" value="3"
            label="How many features having extreme loadings should be labelled on cov-vs.-cor plot"
            help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/>

          <has_text text="5.86655640" />
          <has_text text="0.2111623" />
          <has_text text="0.0488654" />
        </assert_contents>
      </output>
      <output name="contrast_salience">
        <assert_contents>
          <!-- column-labels line -->
          <has_text text="featureID" />
          <has_text text="salientLevel" />

          <has_text text="flower_yes" />
          <has_text text="0.58655260" />
          <has_text text="4.414469" />
          <has_text text="518.1656" />
          <has_text text="368.59817" />
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[

    ]]></citation>
    <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
    <citation type="doi">10.1021/ac0713510</citation>
  </citations>
  <!--
     vim:noet:sw=2:ts=2
-->
</tool>

10:9a52306991b3

<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.14">
    <description>OPLS-DA Contrasts of Univariate Results</description>
    <macros>
        <xml name="paramPairSigFeatOnly">
            <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
                label="Retain only pairwise-significant features"

            help="sample metadata, one row per sample" />
        <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)"
            type="data" help="variable metadata, one row per variable" />
        <param name="facC" type="text"
            label="Factor of interest"
            help="REQUIRED - The name of the column of sampleMetadata corresponding to the qualitative variable used to define the contrasts.  Except when the 'Univariate Significance-test' is set to 'none', this also must be a portion of the column names in the variableMetadata file.">
            <sanitizer>
                <valid initial="string.letters">
                    <add preset="string.digits"/>
                    <add value="&#46;"    /> <!-- dot, period -->
                    <add value="&#95;"    /> <!-- underscore -->
                    <!-- R does not permit dashes in column names; neither does SQL -->
                </valid>
            </sanitizer>
        </param>
        <conditional name="signif_test">
            <param name="tesC" label="Univariate significance-test" type="select" help="Either 'none' or the name of the statistical test that was run by the 'Univariate' tool to produce the variableMetadata file; that name must also be a portion of the column names in that file.">
                <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
                <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
                <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>

                    <add value="&#63;"  /> <!-- ? what, question mark -->
                    <add value="&#91;"  /> <!-- [ l-squib, left-squre-bracket -->
                    <add value="&#92;"  /> <!-- \ whack, backslash -->
                    <add value="&#93;"  /> <!-- ] r-squib, right-squre-bracket -->
                    <add value="&#94;"  /> <!-- ^ hat, caret -->
                    <add value="&#95;"  /> <!-- underscore -->
                    <add value="&#123;" /> <!-- { l-cube, left-curly-bracket -->
                    <add value="&#124;" /> <!-- | pipe -->
                    <add value="&#125;" /> <!-- } r-cube, right-curly-bracket -->
                    <!-- IMPORTANT - Note that single and double quotes are not part of this list; they have the potential to make the 'command' section insecure or broken. -->
                </valid>
            </sanitizer>
        </param>
        <param name="matchingC" label="Level-name matching" type="select" help="How to specify level-names generically. (See help below for details on using wild cards or regular expressions.)">
            <option value="none">do no generic matching</option>
            <option value="wildcard" selected="true">use wild-cards for matching level-names (default)</option>
            <option value="regex">use regular expressions for matching level-names</option>
        </param>
        <param name="labelFeatures" type="text" value="3"
            label="How many features having extreme loadings should be labelled on cov-vs.-cor plot"
            help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/>

          <has_text text="5.86655640" />
          <has_text text="0.2111623" />
          <has_text text="0.0488654" />
        </assert_contents>
      </output>
      <!-- test #4 -->
      <output name="contrast_salience">
        <assert_contents>
          <!-- column-labels line -->
          <has_text text="featureID" />
          <has_text text="salientLevel" />

          <has_text text="flower_yes" />
          <has_text text="0.58655260" />
          <has_text text="4.414469" />
          <has_text text="518.1656" />
          <has_text text="368.59817" />
        </assert_contents>
      </output>
    </test>
    <!-- test #5 -->
    <test>
      <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
      <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
      <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
      <param name="tesC" value="none"/>
      <param name="facC" value="k._10"/>
      <param name="labelFeatures" value="3"/>
      <param name="levCSV" value="k1,k.2"/>
      <param name="matchingC" value="none"/>
      <output name="contrast_corcov">
        <assert_contents>
          <!-- column-labels line -->
          <has_text text="featureID" />
          <has_text text="factorLevel1" />
          <has_text text="factorLevel2" />
          <has_text text="correlation" />
          <has_text text="covariance" />
          <has_text text="vip4p" />
          <has_text text="vip4o" />
          <!-- first matched line -->
          <has_text text="M349.2383T700" />
          <has_text text="-0.37867079" />
          <has_text text="-37.71066" />
          <has_text text="0.5246766" />
          <has_text text="0.0103341" />
          <!-- second matched line -->
          <has_text text="M207.9308T206" />
          <has_text text="0.31570433" />
          <has_text text="5.86655640" />
          <has_text text="0.2111623" />
          <has_text text="0.0488654" />
        </assert_contents>
      </output>
    </test>
    <!-- test #6 -->
    <test>
      <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
      <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
      <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
      <param name="tesC" value="none"/>
      <param name="facC" value="k._10"/>
      <param name="labelFeatures" value="3"/>
      <param name="levCSV" value="k_3,k-4"/>
      <param name="matchingC" value="none"/>
      <output name="contrast_corcov">
        <assert_contents>
          <!-- column-labels line -->
          <has_text text="featureID" />
          <has_text text="factorLevel1" />
          <has_text text="factorLevel2" />
          <has_text text="correlation" />
          <has_text text="covariance" />
          <has_text text="vip4p" />
          <has_text text="vip4o" />
          <!-- first matched line -->
          <has_text text="M349.2383T700" />
          <has_text text="-0.0435663" />
          <has_text text="-1.9068114" />
          <has_text text="0.0304592" />
          <has_text text="0.104748883" />
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[

    ]]></citation>
    <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
    <citation type="doi">10.1021/ac0713510</citation>
  </citations>
  <!--
     vim:et:sw=4:ts=4
-->
</tool>