Mercurial > repos > ebi-gxa > scmap_get_std_output

comparison scmap_get_std_output.xml @ 7:2f63b1cd9122 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"
author ebi-gxa
date Fri, 27 Nov 2020 13:42:47 +0000
parents 0d713384d8d8
children 601a933714f1
comparison
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6:0d713384d8d8 7:2f63b1cd9122
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 "${include_scores}" --index '${index}' --tool '${tool}' --sim-col-name "${sim_col_name}" 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}"
9 #if $index
10 --index "${index}"
11 #end if
9 ]]></command> 12 ]]></command>
10 <inputs> 13 <inputs>
11 <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" /> 14 <param type="data" name="input_predictions_file" label="Scmap predictions file in text format" format="txt" help="Path to the predictions file in text format" />
12 <param type="boolean" name="include_scores" checked="false" label="Should prediction scores be included?" help="Boolean indicating whether similarity scores should be included in the final output" /> 15 <param type="boolean" name="include_scores" checked="false" label="Should prediction scores be included?" help="Boolean indicating whether similarity scores should be included in the final output" />
13 <param type="data" name="index" label="Scmap index object" format="rdata" help="Scmap index object in rdata format" /> 16 <param type="data" name="index" label="Scmap index object" optional="true" format="rdata" help="Scmap index object in rdata format" />
14 <param type="select" name="tool" label="Tool used (cell/cluster)" help="What tool was used - scmap-cell or scmap-cluster?"> 17 <param type="select" name="tool" label="Tool used (cell/cluster)" help="What tool was used - scmap-cell or scmap-cluster?">
15 <option value="scmap-cell">Scmap-cell</option> 18 <option value="scmap-cell">Scmap-cell</option>
16 <option value="scmap-cluster">Scmap-cluster</option> 19 <option value="scmap-cluster">Scmap-cluster</option>
17 </param> 20 </param>
18 <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" /> 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" />
20 <outputs> 23 <outputs>
21 <data name="output_predictions_file" format="txt" /> 24 <data name="output_predictions_file" format="txt" />
22 </outputs> 25 </outputs>
23 <tests> 26 <tests>
24 <test> 27 <test>
25 <param name="input_predictions_file" value="project_cluster.csv" /> 28 <param name="input_predictions_file" value="closest_cells_clusters.tsv" />
26 <param name="include_scores" value="TRUE" /> 29 <param name="include_scores" value="TRUE" />
27 <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" /> 30 <output name="output_predictions_file" value="scmap_output_tbl.txt" compare="sim_size" />
28 </test> 31 </test>
29 </tests> 32 </tests>
30 <help><![CDATA[ 33 <help><![CDATA[