comparison ct_combine_tool_outputs.xml @ 2:a565cf41330b draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c6a3af3aa798c106d1a8f3e2bf1aef5251d0bb7e"
author ebi-gxa
date Mon, 27 Apr 2020 09:26:42 -0400
parents 7c7d1ef36bf6
children 44b6219cba2d
comparison
equal deleted inserted replaced
1:dc68e75e8ae3 2:a565cf41330b
8 mkdir -p input_dir; 8 mkdir -p input_dir;
9 #for $table in $input_tables: 9 #for $table in $input_tables:
10 cp '$table' input_dir/; 10 cp '$table' input_dir/;
11 #end for 11 #end for
12 12
13 combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --exclusions "${exclusions}" --scores "${scores}" --output-table "${output_table}" ]]></command> 13 combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}"
14
15 #if $exclusions
16 --exclusions "${exclusions}"
17 #end if
18 ]]></command>
14 <inputs> 19 <inputs>
15 <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="tsv" help="Standardised tables obtained from multiple classifiers" /> 20 <param type="data" name="input_tables" label="Tables with predicted labels" multiple="true" format="txt" help="Standardised tables obtained from multiple classifiers" />
16 <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" /> 21 <param type="integer" name="top_labels_num" label="Number of top labels" value='3' help="Number of top labels to select" />
17 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" /> 22 <param type="data" name="exclusions" label="Exclusions file" format="yml" optional="true" help="Yaml file with trivial terms and unlabelled cells" />
18 <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" /> 23 <param type="boolean" name="scores" label="scores" checked="false" help="Are scores included into the tool outpus?" />
19 </inputs> 24 </inputs>
20 <outputs> 25 <outputs>
21 <data name="output_table" format="tsv" /> 26 <data name="output_table" format="txt" />
22 </outputs> 27 </outputs>
23 <tests> 28 <tests>
24 <test> 29 <test>
25 <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" /> 30 <param name="input_tables" value="prod_outputs_scpred/E-MTAB-6386_scpred_final-labs.tsv,prod_outputs_scpred/OTHER-DATASET_scpred_final-labs.tsv" />
26 <param name="scores" value="TRUE" /> 31 <param name="scores" value="TRUE" />