comparison garnett_check_markers.xml @ 0:d2aace2bb87f draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4c3dfa7bbd82d702e7e8187c7556f3289804cb49"
author ebi-gxa
date Wed, 08 Apr 2020 06:17:49 -0400
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children c00e672eadbc
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-1:000000000000 0:d2aace2bb87f
1 <tool id="garnett_check_markers" name="Garnett - check markers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Check marker file to filter out markers of suboptimal quality</description>
3 <macros>
4 <import>garnett_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 garnett_check_markers.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cds-gene-id-type '${cds_gene_id_type}' --marker-file-gene-id-type '${marker_file_gene_id_type}' --marker-output-path '${marker_output_path}' --plot-output-path '${plot_output_path}' --propogate-markers '${propogate_markers}' --classifier-gene-id-type '${classifier_gene_id_type}'
9 ]]></command>
10 <inputs>
11 <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
12 <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types.
13 See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" />
14 <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" />
15 <param type="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" />
16 <param type="text" name="marker_file_gene_id_type" label="Marker gene id type" value="ENSEMBL" help="Format of the gene IDs in your marker file" />
17 <param type="boolean" name="propogate_markers" checked="true" label="propogate markers" help="Should markers from child nodes of a cell type be used
18 in finding representatives of the parent type?" />
19 <param type="text" name="classifier_gene_id_type" label="Classifier gene ID type" value="ENSEMBL" help="The type of gene ID that will be used in the classifier. If possible for your organism, this should be 'ENSEMBL', which is the default." />
20 </inputs>
21 <outputs>
22 <data name="marker_output_path" format="txt" />
23 <data name="plot_output_path" format="png" />
24 </outputs>
25 <tests>
26 <test>
27 <param name="cds_object" value="garnett_cds.rds" />
28 <param name="marker_file_path" value="markers_transformed.txt" />
29 <output name="marker_output_path" value="marker_check.txt" compare="sim_size" />
30 </test>
31 </tests>
32 <help><![CDATA[
33 @HELP@
34
35 @VERSION_HISTORY@
36 ]]></help>
37 <expand macro="citations" />
38 </tool>
39