Mercurial > repos > ebi-gxa > ct_get_tool_perf_table

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 8c1bd2ab8a3f988e205677a3bb1ffda1e5694fe1"
author ebi-gxa
date Wed, 17 Jun 2020 16:28:14 +0000
parents 17a46a7e4fbb
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1 <tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>Get performance table for a list of outputs generated by various tools</description>
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3 <macros>
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4 <import>ct_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 mkdir -p input_dir;
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9 #for $input_file in $input_files:
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10 cp '$input_file' input_dir/;
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11 #end for
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13 ln -s $'${ontology_graph}' cl-basic.obo;
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14
2
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15 get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}"
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16
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17 #if $exclusions
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18 --exclusions "${exclusions}"
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19 #end if
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20 #if $parallel
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21 --parallel "${parallel}"
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22 #end if
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23 #if $include_sem_siml
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24 --include-sem-siml "${include_sem_siml}"
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25 #end if
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26 #if $barcode_col_ref
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27 --barcode-col-ref "${barcode_col_ref}"
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28 #end if
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29 #if $barcode_col_pred
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30 --barcode-col-pred "${barcode_col_pred}"
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31 #end if
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32 #if $label_col_ref
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33 --label-column-ref "${label_col_ref}"
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34 #end if
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35 #if $label_col_pred
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36 --label-column-pred "${label_col_pred}"
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37 #end if
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38 #if $semantic_sim_metric
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39 --semantic-sim-metric "${semantic_sim_metric}"
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40 #end if
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41
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42 ]]></command>
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43 <inputs>
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44 <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" />
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45 <param type="data" name="ref_file" label="Reference metadata file" format="txt" help="Metadata file with reference labels" />
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46 <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" />
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47 <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" />
0
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48 <param type="data" name="exclusions" label="Exclusions" format="yml" optional="true" help="Config file with exclusions" />
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49 <param type="data" name="ontology_graph" label="Ontology graph" optional="true" format="obo" help="Ontology graph to run semantis similarity computations" />
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50 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" />
0
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51 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" />
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52 <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" />
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53 <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" />
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54 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" />
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55 <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" />
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56 <expand macro="sem_siml_options" />
0
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57 </inputs>
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58 <outputs>
3
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59 <data name="output_path" format="txt" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input_files" value="results_dir/garnett_output.txt,results_dir/scmap-cell_output.txt,results_dir/scmap-cluster_output.txt,results_dir/scpred_output.txt" />
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64 <param name="ref_file" value="reference_sdrf.tsv" />
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65 <param name="ontology_graph" value="cl-basic.obo" />
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66 <param name="lab_cl_mapping" value="label_cl_dict.rds" />
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67 <param name="parallel" value="TRUE" />
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68 <param name="exclusions" value="exclusions.yml" />
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69 <param name="barcode_col_ref" value="Assay" />
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70 <param name="barcode_col_pred" value="cell_id" />
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71 <param name="label_col_ref" value="Sample.Characteristic.cell.type." />
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72 <param name="label_col_pred" value="predicted_label" />
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73 <output name="output_path" file="tool_perf_table.tsv" compare="sim_size" />
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 @HELP@
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78
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79 @VERSION_HISTORY@
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80 ]]></help>
01b2e83311b2 "planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2"
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81 <expand macro="citations" />
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82 </tool>