| Previous changeset 4:32101a7373ae (2020-06-17) Next changeset 6:00abf723fc87 (2020-07-23) |
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Commit message:
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 4a2a09dd40519b17c68456e69a0a683296d6ee53" |
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modified:
ct_get_consensus_outputs.xml |
| b |
| diff -r 32101a7373ae -r 87d54692a537 ct_get_consensus_outputs.xml --- a/ct_get_consensus_outputs.xml Wed Jun 17 12:29:44 2020 -0400 +++ b/ct_get_consensus_outputs.xml Mon Jul 13 07:24:08 2020 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@"> +<tool id="ct_get_consensus_outputs" name="Cell types - get consensus outputs" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> <description>Get consensus outputs across multiple tools</description> <macros> <import>ct_macros.xml</import> @@ -9,14 +9,18 @@ #for $table in $input_tables: cp '$table' input_dir/; #end for - - ln -s $'${ontology_graph}' cl-basic.obo; - get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --ontology-graph cl-basic.obo --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" + get_consensus_output.R --input-dir input_dir --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}" --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" #if $tool_table --tool-table "${tool_table}" #end if - #if $include-sem-siml + #if $ontology_graph + --ontology-graph "${ontology_graph}" + #end if + #if $tmpdir + --tmpdir "${tmpdir}" + #end if + #if $include_sem_siml --include-sem-siml "${include_sem_siml}" #end if #if $parallel @@ -28,13 +32,13 @@ #if $exclusions --exclusions "${exclusions}" #end if - #if $semantic_sim_metric - --semantic-sim-metric "${semantic_sim_metric}" + #if $sem_siml_metric + --semantic-sim-metric "${sem_siml_metric}" #end if ]]></command> <inputs> <param type="data" name="input_tables" label="Aggregated tables" format="txt" multiple="true" help="Aggregated prediction tables from multiple tools" /> - <param type="data" name="tool_table" format="txt" label="Tools table" help="Table with tools performance metrics" /> + <param type="data" name="tool_table" format="txt" optional="true" label="Tool performance table" help="Table with tools performance metrics" /> <param type="boolean" name="parallel" label="Parallel execution" checked="false" help="Should the table values be computed in parallel?" /> <param type="text" name="tmpdir" label="Tmpdir for caching" optional="true" help="Temporary directory for caching" /> <param type="boolean" name="include_sem_siml" label="Include Semantic Similarity" checked="false" help="Should semantic similarity be included in calculation of combined score?" /> |