Mercurial > repos > ebi-gxa > garnett_transform_markers
view garnett_transform_markers.xml @ 0:2142ecf6ff02 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 06:18:13 -0400 |
parents | |
children | 211241c50ccf |
line wrap: on
line source
<tool id="garnett_transform_markers" name="Garnett - transform markes" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Transform marker files from Single Cell Expression Atlas format to that compatible with Garnett</description> <macros> <import>garnett_macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}' --pval-col '${pval_col}' --pval-threshold '${pval_threshold}' --groups-col '${groups_col}' --gene-names '${gene_names}' --garnett-marker-file '${garnett_marker_file}' ]]></command> <inputs> <param type="data" name="input_marker_file" format="txt" label="Input marker file" help="Path to the SCXA-style marker gene file in .txt format" /> <param type="data" name="marker_list" format="rdata" label="Marker list object" help="Path to a serialised object containing marker genes" /> <param type="text" name="pval_col" value="pvals" label="p-value column name" help="Column name of marker p-values" /> <param type="float" name="pval_threshold" value="0.05" label="p-value threshold" help="Cut-off p-value for marker genes" /> <param type="text" name="groups_col" value="groups" label="groups column" help="Column name of cell groups (i.e. cluster IDs or cell types) in marker file" /> <param type="text" name="gene_names" value="names" label="gene names" help="Column containing gene names in marker file" /> </inputs> <outputs> <data name="garnett_marker_file" format="txt" /> </outputs> <tests> <test> <param name="input_marker_file" value="ref_marker_genes.txt" /> <param name="marker_list" value="marker_list.rds" /> <output name="garnett_marker_file" file="markers_transformed.txt" compare="sim_size"/> </test> </tests> <help><![CDATA[ @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations" /> </tool>