Mercurial > repos > iuc > raceid_filtnormconf

comparison raceid_filtnormconf.xml @ 6:43c146e25a43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 53916f6803b93234f992f5fd4fad61d7013d82af"
author iuc
date Thu, 15 Apr 2021 19:00:38 +0000
parents 7608d5faee41
children d45f092caf24
comparison
equal deleted inserted replaced
5:7608d5faee41 6:43c146e25a43
1 <tool id="raceid_filtnormconf" name="Initial processing using RaceID" version="@VERSION_RACEID@.@VERSION_WRAPPER@" > 1 <tool id="raceid_filtnormconf" name="Initial processing using RaceID" version="@VERSION_RACEID@+galaxy@VERSION_WRAPPER@" >
2 <description>performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data</description> 2 <description>performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>macros_cheetah.xml</import> 5 <import>macros_cheetah.xml</import>
6 </macros> 6 </macros>
25 <expand macro="sanitize_string_vector" /> 25 <expand macro="sanitize_string_vector" />
26 </param> 26 </param>
27 <param name="ccor" type="float" value="0.4" label="CCor" help="Correlation coefficient used as a threshold for determining correlated genes" /> 27 <param name="ccor" type="float" value="0.4" label="CCor" help="Correlation coefficient used as a threshold for determining correlated genes" />
28 <param name="bmode" type="select" label="Batch Mode" help="Method to regress out batch effects" > 28 <param name="bmode" type="select" label="Batch Mode" help="Method to regress out batch effects" >
29 <option value="RaceID" selected="true" >RaceID</option> 29 <option value="RaceID" selected="true" >RaceID</option>
30 <option value="scran">SCRAN</option> 30 <!-- <option value="scran">SCRAN</option> -->
31 </param> 31 </param>
32 <conditional name="ccc" > 32 <conditional name="ccc" >
33 <param name="use" type="select" label="Perform Cell-cycle correction?" > 33 <param name="use" type="select" label="Perform Cell-cycle correction?" >
34 <option value="yes" >Yes</option> 34 <option value="yes" >Yes</option>
35 <option value="no" selected="true" >No</option> 35 <option value="no" selected="true" >No</option>
118 <param name="knn" value="5" /> 118 <param name="knn" value="5" />
119 <param name="ccor" value="0.5" /> 119 <param name="ccor" value="0.5" />
120 <param name="CGenes" value="Gga3,Ggact,Ggct" /> 120 <param name="CGenes" value="Gga3,Ggact,Ggct" />
121 <param name="FGenes" value="Zxdc,Zyg11a,Zyg11b,Zyx" /> 121 <param name="FGenes" value="Zxdc,Zyg11a,Zyg11b,Zyx" />
122 <param name="LBatch_regexes" value="^I5,^II5,^III5,^IV5d,^V5d" /> 122 <param name="LBatch_regexes" value="^I5,^II5,^III5,^IV5d,^V5d" />
123 <param name="bmode" value="scran" /> 123 <!-- <param name="bmode" value="scran" /> -->
124 <conditional name="ccc" > 124 <conditional name="ccc" >
125 <param name="use" value="yes" /> 125 <param name="use" value="yes" />
126 <param name="pvalue" value="0.05" /> 126 <param name="pvalue" value="0.05" />
127 <param name="quant" value="0.05" /> 127 <param name="quant" value="0.05" />
128 <param name="ncomp" value="3" /> 128 <param name="ncomp" value="3" />