Mercurial > repos > ebi-gxa > scpred_get_feature_space

comparison scpred_get_feature_space.xml @ 5:17325882fa72 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:45:33 +0000
parents 41a316354ffb
children
comparison
equal deleted inserted replaced
4:826f41212307 5:17325882fa72
3 <macros> 3 <macros>
4 <import>scpred_macros.xml</import> 4 <import>scpred_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='requirements' /> 6 <expand macro='requirements' />
7 <command detect_errors='exit_code'><![CDATA[ 7 <command detect_errors='exit_code'><![CDATA[
8 scpred_get_feature_space.R --input-object '${input_object}' --prediction-column '${prediction_column}' --output-path '${output_obj_path}' 8 scpred_get_feature_space.R --input-object '${input_object}' --prediction-column '${prediction_column}' --output-path '${output_obj_path}'
9
10 #if $correction_method
11 --correction-method '${correction_method}'
12 #end if
13 #if $significance_threshold
14 --significance-threshold '${significance_threshold}'
15 #end if
16 #if $reduction_parameter
17 --reduction-parameter '${reduction_parameter}'
18 #end if
9 19
10 #if $explained_var_limit 20
11 --explained-var-limit '${explained_var_limit}'
12 #end if
13 #if $eigenvalue_plot_path
14 --eigenvalue-plot-path '${eigenvalue_plot_path}'
15 #end if
16 ]]></command> 21 ]]></command>
17 <inputs> 22 <inputs>
18 <param type='data' name='input_object' label='Input SCE object' format='rdata' help='Input SCE object in .rds format' /> 23 <param type='data' name='input_object' label='Input Seurat object' format='rdata' help='Input Seurat object in .rds format' />
19 <param type='text' name='prediction_column' label='Prediction column' help='Name of the metadata column that contains training labels' /> 24 <param type='text' name='prediction_column' optional="true" value="cell_type" label='Prediction Column' help='Name of the metadata column that contains training labels' />
20 <param type='float' name='explained_var_limit' label='Limit of explained variance' value="0.01" help='Threshold to filter principal components based on variance explained' /> 25 <param type='text' name='correction_method' label='Correction Method' optional='true' value="fdr" help='Method for mulpiple testing correction' />
26 <param type='float' name='significance_threshold' label='Significance Threshold' optional='true' value="1.0" help='Significance threshold for principal components explaining class identity' />
27 <param type='text' name='reduction_parameter' label='Reduction Parameter' optional='true' value="pca" help='Name of reduction in Seurat objet to be used to determine the feature space. Default: "pca"' />
28
21 </inputs> 29 </inputs>
22 <outputs> 30 <outputs>
23 <data name='output_obj_path' format='rdata' /> 31 <data name='output_obj_path' format='rdata' />
24 <data name='eigenvalue_plot_path' format='png' />
25 </outputs> 32 </outputs>
26 <tests> 33 <tests>
27 <test> 34 <test>
28 <param name="input_object" value="scPred_object.rds" /> 35 <param name="input_object" value="reference_pbmc.rds" />
29 <param name="prediction_column" value="cell_type2" />
30 <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" /> 36 <output name="output_obj_path" file="scPred_feat_space.rds" compare="sim_size" />
31 </test> 37 </test>
32 </tests> 38 </tests>
33 <help><![CDATA[ 39 <help><![CDATA[
34 @HELP@ 40 @HELP@