Mercurial > repos > eschen42 > w4mcorcov
changeset 10:9a52306991b3 draft
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 |
| files | w4mcorcov.xml w4mcorcov_input.R |
| diffstat | 2 files changed, 82 insertions(+), 7 deletions(-) [+] |
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--- a/w4mcorcov.xml Fri Aug 10 11:15:31 2018 -0400 +++ b/w4mcorcov.xml Sat Sep 01 11:33:03 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.13"> +<tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.14"> <description>OPLS-DA Contrasts of Univariate Results</description> <macros> <xml name="paramPairSigFeatOnly"> @@ -68,7 +68,16 @@ 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."/> + 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="." /> <!-- dot, period --> + <add value="_" /> <!-- 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> @@ -111,6 +120,7 @@ <add value="\" /> <!-- \ whack, backslash --> <add value="]" /> <!-- ] r-squib, right-squre-bracket --> <add value="^" /> <!-- ^ hat, caret --> + <add value="_" /> <!-- underscore --> <add value="{" /> <!-- { l-cube, left-curly-bracket --> <add value="|" /> <!-- | pipe --> <add value="}" /> <!-- } r-cube, right-curly-bracket --> @@ -119,8 +129,8 @@ </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="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" @@ -311,6 +321,7 @@ <has_text text="0.0488654" /> </assert_contents> </output> + <!-- test #4 --> <output name="contrast_salience"> <assert_contents> <!-- column-labels line --> @@ -386,6 +397,70 @@ </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[ @@ -750,6 +825,6 @@ <citation type="doi">10.1021/ac0713510</citation> </citations> <!-- - vim:noet:sw=2:ts=2 + vim:et:sw=4:ts=4 --> </tool>
--- a/w4mcorcov_input.R Fri Aug 10 11:15:31 2018 -0400 +++ b/w4mcorcov_input.R Sat Sep 01 11:33:03 2018 -0400 @@ -1,6 +1,6 @@ # read_data_frame - read a w4m data frame, with error handling # e.g., data_matrix_input_env <- read_data_frame(dataMatrix_in, "data matrix input") -read_data_frame <- function(file_path, kind_string, failure_action = failure_action) { +read_data_frame <- function(file_path, kind_string, rdf_failure_action = failure_action) { my.env <- new.env() my.env$success <- FALSE my.env$msg <- sprintf("no message reading %s", kind_string) @@ -14,7 +14,7 @@ } ) if (!my.env$success) { - failure_action(my.env$msg) + rdf_failure_action(my.env$msg) return ( FALSE ) } return (my.env)