Mercurial > repos > lgueguen > sartools
diff abims_sartools_edger.xml @ 0:581d217c7337 draft
Planemo upload
author | lgueguen |
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date | Fri, 22 Jul 2016 05:39:13 -0400 |
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children | d86ccac2a660 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abims_sartools_edger.xml Fri Jul 22 05:39:13 2016 -0400 @@ -0,0 +1,190 @@ +<tool id="sartools_edger" name="SARTools edgeR" version="1.0.0"> + + <!-- [REQUIRED] Tool description displayed after the tool name --> + <description>Compare two or more biological conditions in a RNA-Seq framework with edgeR</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + + + <!-- [REQUIRED] The command to execute --> + <command interpreter="python"><![CDATA[ + + abims_sartools_edger_wrapper.py + ## parameters + @COMMAND_BASIC_PARAMETERS@ + #if str( $advanced_parameters.adv_param ) == "show": + @COMMAND_BATCH_PARAM@ + --alpha $advanced_parameters.alpha + --pAdjustMethod $advanced_parameters.pAdjustMethod + --cpmCutoff $advanced_parameters.cpmCutoff + --geneSelection $advanced_parameters.geneSelection + --normalizationMethod $advanced_parameters.normalizationMethod + --colors $advanced_parameters.colors + #end if + ## 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> + </param> + <when value="hide" /> + <when value="show"> + <expand macro="batch_param" /> + <expand macro="alpha_param" /> + <expand macro="padjustmethod_param" /> + <param name="cpmCutoff" type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" help="(-m, --cpmCutoff) Set to 0 to disable filtering. Default is 1." /> + <param name="geneSelection" type="select" label="Selection of the features in MDSPlot" help="(-g, --gene.selection) Default is 'pairwise'." > + <option value="pairwise" selected="true">pairwise</option> + <option value="common">common</option> + </param> + <param name="normalizationMethod" type="select" label="Normalization method in calcNormFactors" help="(-n, --normalizationMethod) 'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." > + <option value="TMM" selected="true">TMM</option> + <option value="RLE">RLE</option> + <option value="upperquartile">upperquartile</option> + </param> + <expand macro="colors_param" /> + </when> + </conditional> + + </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, 10 features --> + <param name="targetFile" dbkey="?" value="target_small.txt" /> + <param name="rawDir" value="raw_small.zip" dbkey="?" ftype="zip"/> + <param name="adv_param" value="show"/> + <output name="log"> + <assert_contents> + <has_text text="KO vs WT 5 4 9" /> + <has_text text="HTML report created" /> + </assert_contents> + </output> + </test> +<!-- <test> +--> <!-- NOT WORKING YET: Test with 3 conditions, 3 replicates, 10 features, with batch effect --> +<!-- <param name="targetFile" dbkey="?" value="targetT048_small.txt" /> + <param name="rawDir" value="rawT048_small.zip" dbkey="?" ftype="no_unzip.zip"/> + <param name="condRef" value="T0"/> + <param name="adv_param" value="show"/> + <param name="condition" value="true"/> + <output name="tables_html" file="SARTools_edgeR_targetT048_small_tables.html" lines_diff="12"> + <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0_small.complete.txt"/> + <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0_small.complete.txt"/> + <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4_small.complete.txt"/> + </output> + </test> +--> <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 2691 2713 5404" /> + <has_text text="HTML report created" /> + </assert_contents> + </output> + </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="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"/> + <output name="tables_html" file="SARTools_edgeR_targetT048_tables.html" lines_diff="14"> + <extra_files type="file" name="T4vsT0.complete.txt" value="SARTools_edgeR_T4vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT0.complete.txt" value="SARTools_edgeR_T8vsT0.complete.txt"/> + <extra_files type="file" name="T8vsT4.complete.txt" value="SARTools_edgeR_T8vsT4.complete.txt"/> + </output> + </test> +--> </tests> + + <!-- [OPTIONAL] Help displayed in Galaxy --> + <help><![CDATA[ + +@HELP_AUTHORS@ + +============== +SARTools edgeR +============== + +----------- +Description +----------- + +@HELP_DESCRIPTION@ + + +----------- +Input files +----------- + +@HELP_INPUT_FILES@ + + +---------- +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); + * **pAdjustMethod:** p-value adjustment method for multiple testing [4, 5] ("BH" by default, "BY" or any value of p.adjust.methods); + * **cpmCutoff:** counts-per-million cut-off to filter low counts (default is 1, set to 0 to disable filtering); + * **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common); + * **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile"; + * **colors:** colors used for the figures (one per biological condition), 8 are given by default. + + +------------ +Output files +------------ + +@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. + +[2] S. Anders. HTSeq: Analysing high-throughput sequencing data with Python. http://www-huber.embl.de/users/anders/HTSeq/, 2011. + +[3] S. Anders, P.-T. Pyl, and W. Huber. HTSeq - A Python framework to work with high-throughput sequencing data. bioRxiv preprint, 2014. URL: http://dx.doi.org/10.1101/002824. + +[4] Y. Benjamini and Y. Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B, 57:289–300, 1995. + +[5] 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> + + <citations> + <expand macro="common_citations" /> + </citations> + +</tool>