Mercurial > repos > lgueguen > sartools
diff abims_sartools_deseq2.xml @ 4:05c9b1a7f44e draft default tip
Uploaded new release 1.7.3
| author | lgueguen |
|---|---|
| date | Thu, 07 Jan 2021 11:12:01 +0000 |
| parents | de6d0b7c17af |
| children |
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--- a/abims_sartools_deseq2.xml Mon Oct 01 05:07:56 2018 -0400 +++ b/abims_sartools_deseq2.xml Thu Jan 07 11:12:01 2021 +0000 @@ -1,114 +1,96 @@ -<tool id="sartools_deseq2" name="SARTools DESeq2" version="@WRAPPER_VERSION@.0"> +<tool id="sartools_deseq2" name="SARTools DESeq2" version="@TOOL_VERSION@+galaxy0"> - <!-- [REQUIRED] Tool description displayed after the tool name --> <description>Compare two or more biological conditions in a RNA-Seq framework with DESeq2</description> <macros> - <import>macros.xml</import> + <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> - <!-- [REQUIRED] The command to execute --> - <command interpreter="python"><![CDATA[ - - abims_sartools_deseq2_wrapper.py - ## parameters - @COMMAND_BASIC_PARAMETERS@ - #if str( $advanced_parameters.adv_param ) == "show": - @COMMAND_BATCH_PARAM@ - --fitType $advanced_parameters.fitType - --cooksCutoff $advanced_parameters.cooksCutoff - --independentFiltering $advanced_parameters.independentFiltering - --alpha $advanced_parameters.alpha - --pAdjustMethod $advanced_parameters.pAdjustMethod - --typeTrans $advanced_parameters.typeTrans - --locfunc $advanced_parameters.locfunc - --colors $advanced_parameters.colors - --forceCairoGraph $advanced_parameters.forceCairoGraph - #end if - ## ouputs - @COMMAND_OUTPUTS@ + <command><![CDATA[ + +python '$__tool_directory__/abims_sartools_deseq2_wrapper.py' +## parameters +@COMMAND_BASIC_PARAMETERS@ +@COMMAND_BATCH_PARAM@ +--fitType '$advanced_parameters.fitType' +--cooksCutoff '$advanced_parameters.cooksCutoff' +--independentFiltering '$advanced_parameters.independentFiltering' +--alpha '$advanced_parameters.alpha' +--pAdjustMethod '$advanced_parameters.pAdjustMethod' +--typeTrans '$advanced_parameters.typeTrans' +--locfunc '$advanced_parameters.locfunc' +--colors "'$advanced_parameters.colors'" +--forceCairoGraph '$advanced_parameters.forceCairoGraph' +## ouputs +@COMMAND_OUTPUTS@ ]]></command> - <!-- [REQUIRED] Input files and tool parameters --> <inputs> <expand macro="basic_parameters" /> - - <conditional name="advanced_parameters" > - <param name="adv_param" type="select" label="Advanced Parameters" help="" > - <option value="hide" selected="true">Hide</option> - <option value="show">Show</option> + + <section name="advanced_parameters" title="Advanced Parameters" expanded="false"> + <expand macro="batch_param" /> + <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." > + <option value="parametric" selected="true">parametric</option> + <option value="local">local</option> + <option value="mean">mean</option> </param> - <when value="hide" /> - <when value="show"> - <expand macro="batch_param" /> - <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." > - <option value="parametric" selected="true">parametric</option> - <option value="local">local</option> - <option value="mean">mean</option> - </param> - <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/> - <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/> - <expand macro="alpha_param" /> - <expand macro="padjustmethod_param" /> - <param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." > - <option value="VST" selected="true">VST</option> - <option value="rlog">rlog</option> - </param> - <param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." > - <option value="median" selected="true">median</option> - <option value="shorth">shorth</option> - </param> - <expand macro="colors_param" /> - <expand macro="forceCairoGraph_param" /> - </when> - </conditional> + <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/> + <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/> + <expand macro="alpha_param" /> + <expand macro="padjustmethod_param" /> + <param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." > + <option value="VST" selected="true">VST</option> + <option value="rlog">rlog</option> + </param> + <param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." > + <option value="median" selected="true">median</option> + <option value="shorth">shorth</option> + </param> + <expand macro="colors_param" /> + <expand macro="forceCairoGraph_param" /> + </section> </inputs> - <!-- [REQUIRED] Output files --> <outputs> <expand macro="outputs" /> </outputs> - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> <!-- Test with 2 conditions, 2 replicates, 8217 features --> <param name="targetFile" dbkey="?" value="target.txt" /> <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/> - <param name="adv_param" value="show"/> <output name="log"> <assert_contents> - <has_text text="KO vs WT 0.1 171" /> + <has_text text="KO vs WT 0.1 171" /> <has_text text="KO vs WT 2583 2663 5246" /> <has_text text="HTML report created" /> </assert_contents> </output> </test> -<!-- <test> +<!-- <test> --> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10160 features, with batch effect --> -<!-- <param name="targetFile" dbkey="?" value="targetT048.txt" /> +<!-- <param name="targetFile" dbkey="?" value="targetT048.txt" /> <param name="rawDir" value="rawT048.zip" dbkey="?" ftype="no_unzip.zip"/> - <param name="condRef" value="T0"/> - <param name="adv_param" value="show"/> - <param name="condition" value="true"/> + <param name="condRef" value="T0"/> + <param name="condition" value="true"/> <output name="tables_html" file="SARTools_DESeq2_targetT048_tables.html" lines_diff="14"> - <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/> - <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/> - <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/> - </output> + <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_DESeq2_T4vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_DESeq2_T8vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_DESeq2_T8vsT4.complete.txt"/> + </output> </test> ---> </tests> +--> </tests> - <!-- [OPTIONAL] Help displayed in Galaxy --> <help><![CDATA[ @HELP_AUTHORS@ @@ -135,17 +117,17 @@ Parameters ---------- - @HELP_BASIC_PARAMETERS@ - * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account); - * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05); - * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local"); - * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4]; - * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5]; - * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods); - * **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation); - * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package); - * **colors:** colors used for the figures (one per biological condition), 8 are given by default. - * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo"). + @HELP_BASIC_PARAMETERS@ + * **batch:** adjustment variable to use as a batch effect, must be a column of the target file (NULL if no batch effect needs to be taken into account); + * **alpha:** significance threshold applied to the adjusted p-values to select the differentially expressed features (default is 0.05); + * **fitType:** type of model for the mean-dispersion relationship ("parametric" by default, or "local"); + * **cooksCutoff:** TRUE (default) of FALSE to execute or not the detection of the outliers [4]; + * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5]; + * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods); + * **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation); + * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package); + * **colors:** colors used for the figures (one per biological condition), 8 are given by default. + * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo"). ------------ @@ -154,7 +136,7 @@ @HELP_OUTPUT_FILES@ - + --------------------------------------------------- [1] G.-K. Smyth. Limma: linear models for microarray data. In R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, and W. Huber, editors, Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. Springer, New York, 2005. @@ -172,27 +154,27 @@ [7] Y. Benjamini and D. Yekutieli. The control of the false discovery rate in multiple testing under dependency. Ann. Statist., 29(4):1165–1188, 2001. - ]]></help> + ]]></help> - <citations> - <expand macro="common_citations" /> - <citation type="bibtex">@ARTICLE{Cook77, - author = {R.-D. Cook}, - title = {Detection of Influential Observation in Linear Regression}, - journal = {Technometrics}, - year = {1977}, - month = {February} - }</citation> - <citation type="bibtex">@ARTICLE{Bourgon10, - author = {R. Bourgon, R. Gentleman, and W. Huber}, - title = {Independent filtering increases detection power for high-throughput experiments}, - journal = {PNAS}, - year = {2010}, - volume = {107}, - number = {21}, - pages = {9546–9551}, - note = {URL: http://www.pnas.org/content/107/21/9546.long} - }</citation> - </citations> + <citations> + <expand macro="common_citations" /> + <citation type="bibtex">@ARTICLE{Cook77, + author = {R.-D. Cook}, + title = {Detection of Influential Observation in Linear Regression}, + journal = {Technometrics}, + year = {1977}, + month = {February} + }</citation> + <citation type="bibtex">@ARTICLE{Bourgon10, + author = {R. Bourgon, R. Gentleman, and W. Huber}, + title = {Independent filtering increases detection power for high-throughput experiments}, + journal = {PNAS}, + year = {2010}, + volume = {107}, + number = {21}, + pages = {9546–9551}, + note = {URL: http://www.pnas.org/content/107/21/9546.long} + }</citation> + </citations> </tool>