Mercurial > repos > ebi-gxa > scmap_get_std_output

comparison scmap_get_std_output.xml @ 1:656c588b718c draft

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"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 11:24:13 -0400
parents 5f95950c3959
children 0cb98597934b
comparison
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0:5f95950c3959 1:656c588b718c
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 "${include_scores}" --sim-col-name "${sim_col_name}" 8 scmap_get_std_output.R --predictions-file "${input_predictions_file}" --output-table "${output_predictions_file}" --include-scores "${include_scores}" --index '${index}' --tool '${tool}' --sim-col-name "${sim_col_name}"
9 ]]></command> 9 ]]></command>
10 <inputs> 10 <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" /> 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" />
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" /> 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" />
13 <param type="data" name="index" label="Scmap index object" 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?">
15 <option value="scmap-cell">Scmap-cell</option>
16 <option value="scmap-cluster">Scmap-cluster</option>
17 </param>
13 <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" /> 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" />
14 </inputs> 19 </inputs>
15 <outputs> 20 <outputs>
16 <data name="output_predictions_file" format="txt" /> 21 <data name="output_predictions_file" format="txt" />
17 </outputs> 22 </outputs>