Mercurial > repos > ebi-gxa > ct_get_tool_perf_table
comparison ct_get_tool_perf_table.xml @ 5:424f8251a202 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53"
| author | ebi-gxa |
|---|---|
| date | Mon, 13 Jul 2020 07:24:58 -0400 |
| parents | d15f7509077b |
| children | 90d7f30478ee |
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| 4:d15f7509077b | 5:424f8251a202 |
|---|---|
| 1 <tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> | 1 <tool id="ct_get_tool_perf_table" name="Cell types - get tool performance table" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> |
| 2 <description>Get performance table for a list of outputs generated by various tools</description> | 2 <description>Get performance table for a list of outputs generated by various tools</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>ct_macros.xml</import> | 4 <import>ct_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 8 mkdir -p input_dir; | 8 mkdir -p input_dir; |
| 9 #for $input_file in $input_files: | 9 #for $input_file in $input_files: |
| 10 cp '$input_file' input_dir/; | 10 cp '$input_file' input_dir/; |
| 11 #end for | 11 #end for |
| 12 | 12 |
| 13 ln -s $'${ontology_graph}' cl-basic.obo; | 13 get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" |
| 14 | |
| 15 get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --num-cores \${GALAXY_SLOTS:-1} --ontology-graph cl-basic.obo --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" | |
| 16 | 14 |
| 17 #if $exclusions | 15 #if $exclusions |
| 18 --exclusions "${exclusions}" | 16 --exclusions "${exclusions}" |
| 19 #end if | 17 #end if |
| 18 #if $ontology_graph | |
| 19 --ontology-graph "${ontology_graph}" | |
| 20 #end if | |
| 20 #if $parallel | 21 #if $parallel |
| 21 --parallel "${parallel}" | 22 --parallel "${parallel}" |
| 23 #end if | |
| 24 #if $tmpdir | |
| 25 --tmpdir "${tmpdir}" | |
| 22 #end if | 26 #end if |
| 23 #if $include_sem_siml | 27 #if $include_sem_siml |
| 24 --include-sem-siml "${include_sem_siml}" | 28 --include-sem-siml "${include_sem_siml}" |
| 25 #end if | 29 #end if |
| 26 #if $barcode_col_ref | 30 #if $barcode_col_ref |
| 33 --label-column-ref "${label_col_ref}" | 37 --label-column-ref "${label_col_ref}" |
| 34 #end if | 38 #end if |
| 35 #if $label_col_pred | 39 #if $label_col_pred |
| 36 --label-column-pred "${label_col_pred}" | 40 --label-column-pred "${label_col_pred}" |
| 37 #end if | 41 #end if |
| 38 #if $semantic_sim_metric | 42 #if $sem_siml_metric |
| 39 --semantic-sim-metric "${semantic_sim_metric}" | 43 --semantic-sim-metric "${sem_siml_metric}" |
| 40 #end if | 44 #end if |
| 41 | 45 |
| 42 ]]></command> | 46 ]]></command> |
| 43 <inputs> | 47 <inputs> |
| 44 <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" /> | 48 <param type="data" name="input_files" label="Input tables" multiple="true" format="txt" help="Classification tables obtained from multiple classisifiers" /> |
| 50 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> | 54 <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> |
| 51 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> | 55 <param type="data" name="lab_cl_mapping" label="Label - CL term mapping" format="rdata" help="Mapping between cell labels and ontology terms" /> |
| 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" /> | 56 <param type="text" name="barcode_col_ref" label="Reference file barcode field" value='cell_id' help="Name of barcode field in reference metadata file" /> |
| 53 <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" /> | 57 <param type="text" name="barcode_col_pred" label="Predicted file barcode field" value="cell_id" help="Name of barcode field in predictions file" /> |
| 54 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> | 58 <param type="text" name="label_col_ref" label="Reference label column" value="cell_type" help="Label column in reference file" /> |
| 55 <param type="text" name="label_col_pred" label="Predicted file label column" value="pred_label" help="Name of label field in predictions file" /> | 59 <param type="text" name="label_col_pred" label="Predicted file label column" value="predicted_label" help="Name of label field in predictions file" /> |
| 56 <expand macro="sem_siml_options" /> | 60 <expand macro="sem_siml_options" /> |
| 57 </inputs> | 61 </inputs> |
| 58 <outputs> | 62 <outputs> |
| 59 <data name="output_path" format="txt" /> | 63 <data name="output_path" format="txt" /> |
| 60 </outputs> | 64 </outputs> |