| Next changeset 1:dc68e75e8ae3 (2020-04-24) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 941a94360593f8dfb7804834f29fb2642ddd53a2" |
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added:
ct_combine_tool_outputs.xml ct_macros.xml |
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| diff -r 000000000000 -r 7c7d1ef36bf6 ct_combine_tool_outputs.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_combine_tool_outputs.xml Wed Apr 08 11:34:35 2020 -0400 |
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| @@ -0,0 +1,37 @@ +<tool id="ct_combine_tool_outputs" name="Cell types - combine tools outputs" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> + <description>Combine predictions for single tool from multiple datasets</description> + <macros> + <import>ct_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p input_dir; + #for $table in $input_tables: + cp '$table' input_dir/; + #end for + + combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --exclusions "${exclusions}" --scores "${scores}" --output-table "${output_table}" ]]></command> + <inputs> + <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="tsv" help="Standardised tables obtained from multiple classifiers" /> + <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" /> + <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> + <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" /> + </inputs> + <outputs> + <data name="output_table" format="tsv" /> + </outputs> + <tests> + <test> + <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" /> + <param name="scores" value="TRUE" /> + <param name="exclusions" value="exclusions.yml" /> + <output name="output_table" file="combined_results.tsv" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + @HELP@ + + @VERSION_HISTORY@ + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 7c7d1ef36bf6 ct_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ct_macros.xml Wed Apr 08 11:34:35 2020 -0400 |
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| @@ -0,0 +1,35 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.0</token> + <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token> + <token name="@PROFILE@">18.01</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.8">cell-types-analysis</requirement> + <yield/> + </requirements> + </xml> + <xml name="version"> + <version_command><![CDATA[ + conda list | grep cell-types-analysis | egrep -o [0-9]\.[0-9]\.[0-9] + ]]></version_command> + </xml> + <token name="@VERSION_HISTORY@"><![CDATA[ +**Version history** +0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. + ]]></token> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{github-cell-types-analysis.git, + author = {Andrey Solovyev, EBI Gene Expression Team}, + year = {2020}, + title = {Suite of scripts for analysis of scRNA-seq cell type classification tool outputs}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/ebi-gene-expression-group/cell-types-analysis.git}, + } + </citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file |