Mercurial > repos > dfornika > chewbbaca_createschema
changeset 13:35ee71a46436 draft
Uploaded
author | dfornika |
---|---|
date | Fri, 21 Feb 2020 23:28:08 +0000 |
parents | 64a7d9e95445 |
children | 1865476fe1e1 |
files | chewbbaca_createschema.xml |
diffstat | 1 files changed, 33 insertions(+), 6 deletions(-) [+] |
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--- a/chewbbaca_createschema.xml Fri Feb 21 01:55:12 2020 +0000 +++ b/chewbbaca_createschema.xml Fri Feb 21 23:28:08 2020 +0000 @@ -5,9 +5,11 @@ </requirements> <command detect_errors="exit_code"><![CDATA[ mkdir assemblies && + ln -s #for $assembly in $assemblies: - ln -s $assembly assemblies && + '${assembly}' #end for + assemblies && chewBBACA.py CreateSchema --cpu \${GALAXY_SLOTS:-1} -i assemblies @@ -25,7 +27,7 @@ ]]> </command> <inputs> - <param name="assemblies" format="fasta" type="data" multiple="true" label="Assembled genomes (fasta)" /> + <param name="assemblies" format="fasta" type="data_collection" collection_type="list" label="Assembled genomes (fasta)" /> <conditional name="prodigal_training_file_source"> <param name="prodigal_training_file_source_selector" type="select" label="Select a Prodigal training file from your history or use one from a tool data table?"> @@ -36,8 +38,8 @@ <when value="No"/> <when value="tool_data_table"> <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File"> - <options from_data_table="chewbbaca_prodigal_training_files"> - <validator type="no_options" message="No chewBBACA prodigal training files are available" /> + <options from_data_table="prodigal_training_files"> + <validator type="no_options" message="No prodigal training files are available" /> </options> </param> </when> @@ -51,10 +53,35 @@ <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" /> </inputs> <outputs> - <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"/> + <data name="schema" type="list" format="fasta" label="${tool.name}: on ${on_string}: Schema"> + <discover_datasets pattern="__name_and_ext__" format="fasta" directory="schema" /> + </data> + <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz"> + </data> </outputs> <tests> - + <test> + <param name="prodigal_training_file_source_selector" value="history" /> + <param name="prodigal_training_file" value="prodigal_training_files/Streptococcus_agalactiae.trn" /> + <param name="assemblies"> + <collection type="list"> + <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" /> + <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" /> + </collection> + </param> + <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" /> + </test> + <test> + <param name="prodigal_training_file_source_selector" value="tool_data_table" /> + <param name="prodigal_training_file" value="Streptococcus_agalactiae" /> + <param name="assemblies"> + <collection type="list"> + <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" /> + <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" /> + </collection> + </param> + <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" /> + </test> </tests> <help><![CDATA[ ]]>