Mercurial > repos > ebi-gxa > scmap_get_std_output
comparison scmap_get_std_output.xml @ 8:601a933714f1 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75
author | ebi-gxa |
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date | Tue, 23 Apr 2024 07:49:05 +0000 |
parents | 2f63b1cd9122 |
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7:2f63b1cd9122 | 8:601a933714f1 |
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3 <macros> | 3 <macros> |
4 <import>scmap_macros.xml</import> | 4 <import>scmap_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 scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --tool '${tool}' --sim-col-name "${sim_col_name}" | 8 scmap_get_std_output.R |
9 --predictions-file "${input_predictions_file}" | |
10 --output-table "${output_predictions_file}" | |
11 --include-scores "${include_scores}" | |
12 --tool '${tool}' | |
13 --sim-col-name "${sim_col_name}" | |
9 #if $index | 14 #if $index |
10 --index "${index}" | 15 --index "${index}" |
11 #end if | 16 #end if |
12 ]]></command> | 17 ]]></command> |
13 <inputs> | 18 <inputs> |
19 <option value="scmap-cluster">Scmap-cluster</option> | 24 <option value="scmap-cluster">Scmap-cluster</option> |
20 </param> | 25 </param> |
21 <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" /> | 26 <param type="text" name="sim_col_name" value="scmap_cluster_siml" label="Column name of similarity scores" help="Name of column that contains distances between clusters/cells" /> |
22 </inputs> | 27 </inputs> |
23 <outputs> | 28 <outputs> |
24 <data name="output_predictions_file" format="txt" /> | 29 <data name="output_predictions_file" format="tabular" /> |
25 </outputs> | 30 </outputs> |
26 <tests> | 31 <tests> |
27 <test> | 32 <test> |
28 <param name="input_predictions_file" value="closest_cells_clusters.tsv" /> | 33 <param name="input_predictions_file" value="closest_cells_clusters.tsv" /> |
29 <param name="include_scores" value="TRUE" /> | 34 <param name="include_scores" value="TRUE" /> |
30 <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" /> | 35 <output name="output_predictions_file"> |
36 <assert_contents> | |
37 <has_n_lines n="92"/> | |
38 <has_text text="predicted_label"/> | |
39 <has_text text="Zygote..3.RPKM."/> | |
40 </assert_contents> | |
41 </output> | |
31 </test> | 42 </test> |
32 </tests> | 43 </tests> |
33 <help><![CDATA[ | 44 <help><![CDATA[ |
34 Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis. | 45 Generate output tables in tab-separated format compatible with input specified in cell-types-analysis package: https://github.com/ebi-gene-expression-group/cell-types-analysis. |
35 See the example snippet below: | 46 See the example snippet below: |