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annotate scmap_get_std_output.xml @ 8:601a933714f1 draft

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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
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1 <tool id="scmap_get_std_output" name="Scmap get standard output" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Create final output in standard format to allow for downstream analysis of predicted labels by tools of the EBI gene expression group's cell-types-analysis package</description>
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3 <macros>
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4 <import>scmap_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 scmap_get_std_output.R
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9 --predictions-file "${input_predictions_file}"
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10 --output-table "${output_predictions_file}"
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11 --include-scores "${include_scores}"
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12 --tool '${tool}'
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13 --sim-col-name "${sim_col_name}"
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14 #if $index
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15 --index "${index}"
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <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" />
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20 <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" />
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21 <param type="data" name="index" label="Scmap index object" optional="true" format="rdata" help="Scmap index object in rdata format" />
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22 <param type="select" name="tool" label="Tool used (cell/cluster)" help="What tool was used - scmap-cell or scmap-cluster?">
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23 <option value="scmap-cell">Scmap-cell</option>
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24 <option value="scmap-cluster">Scmap-cluster</option>
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25 </param>
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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" />
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27 </inputs>
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28 <outputs>
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29 <data name="output_predictions_file" format="tabular" />
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input_predictions_file" value="closest_cells_clusters.tsv" />
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34 <param name="include_scores" value="TRUE" />
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35 <output name="output_predictions_file">
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36 <assert_contents>
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37 <has_n_lines n="92"/>
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38 <has_text text="predicted_label"/>
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39 <has_text text="Zygote..3.RPKM."/>
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40 </assert_contents>
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41 </output>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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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.
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46 See the example snippet below:
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47 ________________________________________
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48 | cell_id | predicted_label | score |
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49 | ERR2632411 | memory B cell | 0.8 |
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50 ...
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52 @VERSION_HISTORY@
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53 ]]></help>
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54 <expand macro="citations" />
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55 </tool>
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