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comparison w4mcorcov.xml @ 10:9a52306991b3 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552
author eschen42
date Sat, 01 Sep 2018 11:33:03 -0400
parents 06c51af11531
children ddcc33ff3205
comparison
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9:06c51af11531 10:9a52306991b3
1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.13"> 1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.14">
2 <description>OPLS-DA Contrasts of Univariate Results</description> 2 <description>OPLS-DA Contrasts of Univariate Results</description>
3 <macros> 3 <macros>
4 <xml name="paramPairSigFeatOnly"> 4 <xml name="paramPairSigFeatOnly">
5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" 5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
6 label="Retain only pairwise-significant features" 6 label="Retain only pairwise-significant features"
66 help="sample metadata, one row per sample" /> 66 help="sample metadata, one row per sample" />
67 <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)" 67 <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)"
68 type="data" help="variable metadata, one row per variable" /> 68 type="data" help="variable metadata, one row per variable" />
69 <param name="facC" type="text" 69 <param name="facC" type="text"
70 label="Factor of interest" 70 label="Factor of interest"
71 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."/> 71 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.">
72 <sanitizer>
73 <valid initial="string.letters">
74 <add preset="string.digits"/>
75 <add value="&#46;" /> <!-- dot, period -->
76 <add value="&#95;" /> <!-- underscore -->
77 <!-- R does not permit dashes in column names; neither does SQL -->
78 </valid>
79 </sanitizer>
80 </param>
72 <conditional name="signif_test"> 81 <conditional name="signif_test">
73 <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."> 82 <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.">
74 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option> 83 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
75 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option> 84 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
76 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option> 85 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>
109 <add value="&#63;" /> <!-- ? what, question mark --> 118 <add value="&#63;" /> <!-- ? what, question mark -->
110 <add value="&#91;" /> <!-- [ l-squib, left-squre-bracket --> 119 <add value="&#91;" /> <!-- [ l-squib, left-squre-bracket -->
111 <add value="&#92;" /> <!-- \ whack, backslash --> 120 <add value="&#92;" /> <!-- \ whack, backslash -->
112 <add value="&#93;" /> <!-- ] r-squib, right-squre-bracket --> 121 <add value="&#93;" /> <!-- ] r-squib, right-squre-bracket -->
113 <add value="&#94;" /> <!-- ^ hat, caret --> 122 <add value="&#94;" /> <!-- ^ hat, caret -->
123 <add value="&#95;" /> <!-- underscore -->
114 <add value="&#123;" /> <!-- { l-cube, left-curly-bracket --> 124 <add value="&#123;" /> <!-- { l-cube, left-curly-bracket -->
115 <add value="&#124;" /> <!-- | pipe --> 125 <add value="&#124;" /> <!-- | pipe -->
116 <add value="&#125;" /> <!-- } r-cube, right-curly-bracket --> 126 <add value="&#125;" /> <!-- } r-cube, right-curly-bracket -->
117 <!-- 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. --> 127 <!-- 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. -->
118 </valid> 128 </valid>
119 </sanitizer> 129 </sanitizer>
120 </param> 130 </param>
121 <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.)"> 131 <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.)">
122 <option value="none">do no generic matching (default)</option> 132 <option value="none">do no generic matching</option>
123 <option value="wildcard" selected="true">use wild-cards for matching level-names</option> 133 <option value="wildcard" selected="true">use wild-cards for matching level-names (default)</option>
124 <option value="regex">use regular expressions for matching level-names</option> 134 <option value="regex">use regular expressions for matching level-names</option>
125 </param> 135 </param>
126 <param name="labelFeatures" type="text" value="3" 136 <param name="labelFeatures" type="text" value="3"
127 label="How many features having extreme loadings should be labelled on cov-vs.-cor plot" 137 label="How many features having extreme loadings should be labelled on cov-vs.-cor plot"
128 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."/> 138 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."/>
309 <has_text text="5.86655640" /> 319 <has_text text="5.86655640" />
310 <has_text text="0.2111623" /> 320 <has_text text="0.2111623" />
311 <has_text text="0.0488654" /> 321 <has_text text="0.0488654" />
312 </assert_contents> 322 </assert_contents>
313 </output> 323 </output>
324 <!-- test #4 -->
314 <output name="contrast_salience"> 325 <output name="contrast_salience">
315 <assert_contents> 326 <assert_contents>
316 <!-- column-labels line --> 327 <!-- column-labels line -->
317 <has_text text="featureID" /> 328 <has_text text="featureID" />
318 <has_text text="salientLevel" /> 329 <has_text text="salientLevel" />
381 <has_text text="flower_yes" /> 392 <has_text text="flower_yes" />
382 <has_text text="0.58655260" /> 393 <has_text text="0.58655260" />
383 <has_text text="4.414469" /> 394 <has_text text="4.414469" />
384 <has_text text="518.1656" /> 395 <has_text text="518.1656" />
385 <has_text text="368.59817" /> 396 <has_text text="368.59817" />
397 </assert_contents>
398 </output>
399 </test>
400 <!-- test #5 -->
401 <test>
402 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
403 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
404 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
405 <param name="tesC" value="none"/>
406 <param name="facC" value="k._10"/>
407 <param name="labelFeatures" value="3"/>
408 <param name="levCSV" value="k1,k.2"/>
409 <param name="matchingC" value="none"/>
410 <output name="contrast_corcov">
411 <assert_contents>
412 <!-- column-labels line -->
413 <has_text text="featureID" />
414 <has_text text="factorLevel1" />
415 <has_text text="factorLevel2" />
416 <has_text text="correlation" />
417 <has_text text="covariance" />
418 <has_text text="vip4p" />
419 <has_text text="vip4o" />
420 <!-- first matched line -->
421 <has_text text="M349.2383T700" />
422 <has_text text="-0.37867079" />
423 <has_text text="-37.71066" />
424 <has_text text="0.5246766" />
425 <has_text text="0.0103341" />
426 <!-- second matched line -->
427 <has_text text="M207.9308T206" />
428 <has_text text="0.31570433" />
429 <has_text text="5.86655640" />
430 <has_text text="0.2111623" />
431 <has_text text="0.0488654" />
432 </assert_contents>
433 </output>
434 </test>
435 <!-- test #6 -->
436 <test>
437 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
438 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
439 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
440 <param name="tesC" value="none"/>
441 <param name="facC" value="k._10"/>
442 <param name="labelFeatures" value="3"/>
443 <param name="levCSV" value="k_3,k-4"/>
444 <param name="matchingC" value="none"/>
445 <output name="contrast_corcov">
446 <assert_contents>
447 <!-- column-labels line -->
448 <has_text text="featureID" />
449 <has_text text="factorLevel1" />
450 <has_text text="factorLevel2" />
451 <has_text text="correlation" />
452 <has_text text="covariance" />
453 <has_text text="vip4p" />
454 <has_text text="vip4o" />
455 <!-- first matched line -->
456 <has_text text="M349.2383T700" />
457 <has_text text="-0.0435663" />
458 <has_text text="-1.9068114" />
459 <has_text text="0.0304592" />
460 <has_text text="0.104748883" />
386 </assert_contents> 461 </assert_contents>
387 </output> 462 </output>
388 </test> 463 </test>
389 </tests> 464 </tests>
390 <help><![CDATA[ 465 <help><![CDATA[
748 ]]></citation> 823 ]]></citation>
749 <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT --> 824 <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
750 <citation type="doi">10.1021/ac0713510</citation> 825 <citation type="doi">10.1021/ac0713510</citation>
751 </citations> 826 </citations>
752 <!-- 827 <!--
753 vim:noet:sw=2:ts=2 828 vim:et:sw=4:ts=4
754 --> 829 -->
755 </tool> 830 </tool>