Mercurial > repos > ebi-gxa > garnett_classify_cells

comparison garnett_classify_cells.xml @ 1:ad647e1d14dc draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"
author ebi-gxa
date Fri, 24 Apr 2020 11:22:06 -0400
parents 67e6c4455bb8
children
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0:67e6c4455bb8 1:ad647e1d14dc
3 <macros> 3 <macros>
4 <import>garnett_macros.xml</import> 4 <import>garnett_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 garnett_classify_cells.R --cds-object '${cds_object}' --classifier-object '${classifier_object}' --database '${database}' --cds-gene-id-type '${cds_gene_id_type}' --cluster-extend '${cluster_extend}' --rank-prob-ratio '${rank_prob_ratio}' --cds-output-obj '${cds_output_obj}' 8 garnett_classify_cells.R --cds-object '${cds_object}' --classifier-object '${classifier_object}' --database '${database}' --cds-output-obj '${cds_output_obj}'
9
10 #if $cds_gene_id_type
11 --cds-gene-id-type '${cds_gene_id_type}'
12 #end if
13 #if $cluster_extend
14 --cluster-extend '${cluster_extend}'
15 #end if
16 #if $rank_prob_ratio
17 --rank-prob-ratio '${rank_prob_ratio}'
18 #end if
9 ]]></command> 19 ]]></command>
10 <inputs> 20 <inputs>
11 <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" /> 21 <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
12 <param type="data" name="classifier_object" label="classifier object" format="rdata" help="Path to the object of class garnett_classifier, which is either trained via garnett_train_classifier.R or obtained elsewhere" /> 22 <param type="data" name="classifier_object" label="classifier object" format="rdata" help="Path to the object of class garnett_classifier, which is either trained via garnett_train_classifier.R or obtained elsewhere" />
13 <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" /> 23 <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" />