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comparison abims_sartools_deseq2.xml @ 3:de6d0b7c17af draft

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release 1.6.3
author lgueguen
date Mon, 01 Oct 2018 05:07:56 -0400
parents d86ccac2a660
children 05c9b1a7f44e
comparison
equal deleted inserted replaced
2:d86ccac2a660 3:de6d0b7c17af
24 --alpha $advanced_parameters.alpha 24 --alpha $advanced_parameters.alpha
25 --pAdjustMethod $advanced_parameters.pAdjustMethod 25 --pAdjustMethod $advanced_parameters.pAdjustMethod
26 --typeTrans $advanced_parameters.typeTrans 26 --typeTrans $advanced_parameters.typeTrans
27 --locfunc $advanced_parameters.locfunc 27 --locfunc $advanced_parameters.locfunc
28 --colors $advanced_parameters.colors 28 --colors $advanced_parameters.colors
29 --forceCairoGraph $advanced_parameters.forceCairoGraph
29 #end if 30 #end if
30 ## ouputs 31 ## ouputs
31 @COMMAND_OUTPUTS@ 32 @COMMAND_OUTPUTS@
32 33
33 ]]></command> 34 ]]></command>
43 <option value="show">Show</option> 44 <option value="show">Show</option>
44 </param> 45 </param>
45 <when value="hide" /> 46 <when value="hide" />
46 <when value="show"> 47 <when value="show">
47 <expand macro="batch_param" /> 48 <expand macro="batch_param" />
48 <param name="fitType" type="select" label="Mean-variance relationship" help="(-f, --fitType) Type of model for the mean-dispersion relationship. Parametric by default." > 49 <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." >
49 <option value="parametric" selected="true">parametric</option> 50 <option value="parametric" selected="true">parametric</option>
50 <option value="local">local</option> 51 <option value="local">local</option>
52 <option value="mean">mean</option>
51 </param> 53 </param>
52 <param name="cooksCutoff" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" help="(-o, --cooksCutoff) Checked by default."/> 54 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/>
53 <param name="independentFiltering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" help="(-i, --independentFiltering) Checked by default."/> 55 <param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/>
54 <expand macro="alpha_param" /> 56 <expand macro="alpha_param" />
55 <expand macro="padjustmethod_param" /> 57 <expand macro="padjustmethod_param" />
56 <param name="typeTrans" type="select" label="Transformation for PCA/clustering" help="(-T --typeTrans) Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." > 58 <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." >
57 <option value="VST" selected="true">VST</option> 59 <option value="VST" selected="true">VST</option>
58 <option value="rlog">rlog</option> 60 <option value="rlog">rlog</option>
59 </param> 61 </param>
60 <param name="locfunc" type="select" label="Estimation of the size factors" help="(-l --locfunc) 'median' (default) or 'shorth' from the genefilter package." > 62 <param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." >
61 <option value="median" selected="true">median</option> 63 <option value="median" selected="true">median</option>
62 <option value="shorth">shorth</option> 64 <option value="shorth">shorth</option>
63 </param> 65 </param>
64 <expand macro="colors_param" /> 66 <expand macro="colors_param" />
67 <expand macro="forceCairoGraph_param" />
65 </when> 68 </when>
66 </conditional> 69 </conditional>
67 70
68 </inputs> 71 </inputs>
69 72
83 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/> 86 <param name="rawDir" value="raw.zip" dbkey="?" ftype="zip"/>
84 <param name="adv_param" value="show"/> 87 <param name="adv_param" value="show"/>
85 <output name="log"> 88 <output name="log">
86 <assert_contents> 89 <assert_contents>
87 <has_text text="KO vs WT 0.1 171" /> 90 <has_text text="KO vs WT 0.1 171" />
88 <has_text text="KO vs WT 2584 2665 5249" /> 91 <has_text text="KO vs WT 2583 2663 5246" />
89 <has_text text="HTML report created" /> 92 <has_text text="HTML report created" />
90 </assert_contents> 93 </assert_contents>
91 </output> 94 </output>
92 </test> 95 </test>
93 <!-- <test> 96 <!-- <test>
140 * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5]; 143 * **independentFiltering:** TRUE (default) of FALSE to execute or not the independent filtering [5];
141 * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods); 144 * **pAdjustMethod:** p-value adjustment method for multiple testing [6, 7] ("BH" by default, "BY" or any value of p.adjust.methods);
142 * **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); 145 * **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);
143 * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package); 146 * **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package);
144 * **colors:** colors used for the figures (one per biological condition), 8 are given by default. 147 * **colors:** colors used for the figures (one per biological condition), 8 are given by default.
148 * **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
145 149
146 150
147 ------------ 151 ------------
148 Output files 152 Output files
149 ------------ 153 ------------