Mercurial > repos > ebi-gxa > update_marker_file

comparison update_marker_file.xml @ 0:8ee96cde3643 draft

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"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 06:32:25 -0400
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children 5036928f60bc
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-1:000000000000 0:8ee96cde3643
1 <tool id="update_marker_file" name="Garnett - update markers" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Update marker file by filtering out suboptimal markers</description>
3 <macros>
4 <import>garnett_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}' --summary-col '${summary_col}' --cell-type-col '${cell_type_col}' --gene-id-col '${gene_id_col}' --updated-marker-file '${updated_marker_file}'
9 ]]></command>
10 <inputs>
11 <param type="data" name="marker_list_obj" label="Marker list object" format="rdata" help="Serialised object containing markers list produced by garnett_transform_markers" />
12 <param type="data" name="marker_check_file" label="marker check file" format="txt" help="Path to the file with marker gene assessment done by garnett" />
13 <param type="text" name="summary_col" value="summary" label="Name of summary column" help="Marker gene assessment column name" />
14 <param type="text" name="cell_type_col" value="cell_type" label="Name of cell type column" help="Marker gene assessment column name" />
15 <param type="text" name="gene_id_col" value="gene_id" label="Name of gene id column" help="Gene id column name in marker assessment file" />
16 </inputs>
17 <outputs>
18 <data name="updated_marker_file" format="txt" />
19 </outputs>
20 <tests>
21 <test>
22 <param name="marker_list_obj" value="marker_list.rds" />
23 <param name="marker_check_file" value="marker_check.txt" />
24 <output name="updated_marker_file" file="markers_upd.txt" compare="sim_size"/>
25 </test>
26 </tests>
27 <help><![CDATA[
28 @HELP@
29
30 @VERSION_HISTORY@
31 ]]></help>
32 <expand macro="citations" />
33 </tool>