Mercurial > repos > ebi-gxa > update_marker_file
comparison update_marker_file.xml @ 1:5036928f60bc draft
"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 11:23:13 -0400 |
| parents | 8ee96cde3643 |
| children |
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| 0:8ee96cde3643 | 1:5036928f60bc |
|---|---|
| 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 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}' | 8 update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}' --updated-marker-file '${updated_marker_file}' |
| 9 | |
| 10 #if $summary_col | |
| 11 --summary-col '${summary_col}' | |
| 12 #end if | |
| 13 #if $cell_type_col | |
| 14 --cell-type-col '${cell_type_col}' | |
| 15 #end if | |
| 16 #if $gene_id_col | |
| 17 --gene-id-col '${gene_id_col}' | |
| 18 #end if | |
| 9 ]]></command> | 19 ]]></command> |
| 10 <inputs> | 20 <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" /> | 21 <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" /> | 22 <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" /> | 23 <param type="text" name="summary_col" value="summary" label="Name of summary column" help="Marker gene assessment column name" /> |