comparison scmap_get_std_output.xml @ 8:601a933714f1 draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8350493268ce3ced12b1133b9b0f734a288deb75
author ebi-gxa
date Tue, 23 Apr 2024 07:49:05 +0000
parents 2f63b1cd9122
children
comparison
equal deleted inserted replaced
7:2f63b1cd9122 8:601a933714f1
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: