Mercurial > repos > ebi-gxa > scpred_predict_labels

comparison scpred_predict.xml @ 7:b869bb6d4b01 draft default tip

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"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 13:46:06 +0000
parents eca76dd511f4
children
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6:d071810dc6db 7:b869bb6d4b01
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_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --output-path "${output_tbl_path}" 8 scpred_predict.R --input-object "${input_object}" --pred-data "${pred_data}" --normalise-data "${normalise_data}" --recompute-alignment "${recompute_alignment}" --reference-scaling "${reference_scaling}" --output-path "${output_path}"
9 9
10 #if $test_labels 10 #if $normalisation_method
11 --test-labels "${test_labels}" 11 --normalisation-method "${normalisation_method}"
12 #end if 12 #end if
13 #if $cell_types_column 13 #if $scale_factor
14 --cell-types-column "${cell_types_column}" 14 --scale-factor "${scale_factor}"
15 #end if 15 #end if
16 #if $plot_path 16 #if $threshold_level
17 --plot-path "${plot_path}" 17 --threshold-level "${threshold_level}"
18 #end if 18 #end if
19 #if $confusion_table 19 #if $max_iter_harmony
20 --confusion-table "${confusion_table}" 20 --max-iter-harmony "${max_iter_harmony}"
21 #end if 21 #end if
22 22
23 ]]></command> 23 ]]></command>
24 <inputs> 24 <inputs>
25 <param type="data" name="input_object" label="Input SCE object" format="rdata" help="Input SCE object in .rds format" /> 25
26 <param type="data" name="pred_data" label="Matrix with query data" format="rdata" help="Path to the input prediction matrix in .rds format"/> 26 <param type="data" name="input_object" label="Input Seurat Object" format="rdata" help="Input Seurat object in .rds format" />
27 <param type="data" name="test_labels" optional="true" format="txt" label="Test labels" help="Path to the test labels file for evalutation of model performance in text format" /> 27 <param type="data" name="pred_data" label="Query Data Matrix" format="rdata" help="Path to the input prediction matrix in .rds format"/>
28 <param type="text" name="cell_types_column" value="cell_type2" optional="true" label="Cell types column name" help="Column name of true labels in provided metadata file" /> 28 <param type="boolean" checked="false" name="normalise_data" label="Normalise Data" help="Should the predicted expression data be normalised? Default: False"/>
29 <param type="text" name="normalisation_method" optional="true" value="LogNormalize" label="Normalisation Method" help="What normalisation method should be applied to predicted data? Default: LogNormalize" />
30 <param type="integer" name="scale_factor" optional="true" value="1000000" label="Scale Factor" help="What scale factor should be applied? Note: for CPM normalisation, 1e6 is selected by default" />
31 <param type="float" name="threshold_level" optional="true" value="0.8" label="Threshold Level" help="Classification threshold value" />
32 <param type="integer" name="max_iter_harmony" optional="true" value="20" label="Max Iterations" help="Maximum number of rounds to run Harmony. One round of Harmony involves one clustering and one correction step" />
33 <param type="boolean" checked="true" name="recompute_alignment" label="Recompute Alignment" help="Recompute alignment? Useful if scPredict() has already been run. Default: True"/>
34 <param type="boolean" checked="true" name="reference_scaling" label="Reference Scaling" help="Scale new dataset based on means and stdevs from reference dataset before alignment. Default: True"/>
35
29 </inputs> 36 </inputs>
30 <outputs> 37 <outputs>
31 <data name="output_tbl_path" format="txt" /> 38 <data name="output_path" format="rdata" />
32 <data name="plot_path" format="png" />
33 <data name="confusion_table" format="txt" />
34 </outputs> 39 </outputs>
35 <tests> 40 <tests>
36 <test> 41 <test>
37 <param name="input_object" value="scPred_trained.rds" /> 42 <param name="input_object" value="scPred_trained.rds" />
38 <param name="pred_data" value="test_matrix.mtx" /> 43 <param name="normalise_data" value="True" />
39 <param name="test_labels" value="test_metadata.txt" /> 44 <param name="pred_data" value="query_pbmc.rds" />
40 <output name="output_tbl_path" file="predictions_table.txt" compare="sim_size"/> 45 <output name="output_path" file="predicted_data.rds" compare="sim_size" delta="10000000"/>
41 </test> 46 </test>
42 </tests> 47 </tests>
43 <help><![CDATA[ 48 <help><![CDATA[
44 @HELP@ 49 @HELP@
45 50