Mercurial > repos > iuc > spades_rnaviralspades
changeset 7:d5fb354f745d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2
| author | iuc |
|---|---|
| date | Tue, 23 Aug 2022 07:59:16 +0000 |
| parents | 48cf45a53456 |
| children | de1260f8a300 |
| files | macros.xml rnaviralspades.xml |
| diffstat | 2 files changed, 16 insertions(+), 14 deletions(-) [+] |
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--- a/macros.xml Wed Aug 10 13:14:28 2022 +0000 +++ b/macros.xml Tue Aug 23 07:59:16 2022 +0000 @@ -601,34 +601,34 @@ <xml name="out_ag"> <data name="out_ag" format="fastg" from_work_dir="output/assembly_graph.fastg" label="${tool.name} on ${on_string}: Assembly graph"> <filter>'ag' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_ags"> <data name="out_ags" format="txt" from_work_dir="output/assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: Assembly graph with scaffolds"> <filter>'ags' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_cn"> <data name="out_cn" format="fasta" from_work_dir="output/contigs.fasta" label="${tool.name} on ${on_string}: Contigs"> <filter>'cn' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_cp"> <data name="out_cp" format="txt" from_work_dir="output/contigs.paths" label="${tool.name} on ${on_string}: Contigs paths"> <filter>'cp' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_cr"> <!-- some mode combinations create fastq, some fasta --> <collection name="out_cr" type="list" label="${tool.name} on ${on_string}: Corrected reads"> <filter>'cr' in optional_output</filter> - <filter> operation_mode != '--only-assembler'</filter> - <discover_datasets pattern="(?P<designation>.+)\.fastq\.gz" format="fastq" directory="output/corrected"/> - <discover_datasets pattern="(?P<designation>.+)\.fasta\.gz" format="fasta" directory="output/corrected"/> + <filter>'operation_mode' not in vars() or operation_mode != '--only-assembler'</filter> + <discover_datasets pattern="(?P<designation>.+)\.cor\.fastq\.gz" format="fastq" directory="output/corrected"/> + <discover_datasets pattern="(?P<designation>.+)\.cor\.fasta\.gz" format="fasta" directory="output/corrected"/> </collection> </xml> <xml name="out_cs"> @@ -637,7 +637,7 @@ <action name="column_names" type="metadata" default="name,length,coverage"/> </actions> <filter>'cs' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_l"> @@ -648,13 +648,13 @@ <xml name="out_sc"> <data name="out_sc" format="fasta" from_work_dir="output/scaffolds.fasta" label="${tool.name} on ${on_string}: Scaffolds"> <filter>'sc' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_sp"> <data name="out_sp" format="txt" from_work_dir="output/scaffolds.paths" label="${tool.name} on ${on_string}: Scaffolds paths"> <filter>'sp' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_ss"> @@ -663,7 +663,7 @@ <action name="column_names" type="metadata" default="name,length,coverage"/> </actions> <filter>'ss' in optional_output</filter> - <filter> operation_mode != '--only-error-correction'</filter> + <filter>'operation_mode' not in vars() or operation_mode != '--only-error-correction'</filter> </data> </xml> <xml name="out_rs">
--- a/rnaviralspades.xml Wed Aug 10 13:14:28 2022 +0000 +++ b/rnaviralspades.xml Tue Aug 23 07:59:16 2022 +0000 @@ -21,6 +21,7 @@ @OMP_THREADS@ ## run spades.py --rnaviral + $operation_mode -o 'output' @RESOURCES@ @INPUT_READS_MAIN@ @@ -41,6 +42,7 @@ @CORRECTED@ ]]></command> <inputs> + <expand macro="operation_mode" help="To run read error correction, reads should be in FASTQ format."/> <expand macro="input_files_all" format="fastq,fasta,fastq.gz,fastqsanger.gz,fasta.gz" label="FASTQ RNA-seq file(s)"/> <expand macro="input_additional_files_all" format="fastq,fastq.gz,fastqsanger.gz,fasta,fasta.gz" label="FASTQ RNA-seq file(s)"/> <section name="arf" title="Additional read files"> @@ -144,13 +146,13 @@ <has_n_lines n="0"/> </assert_contents> </output> - <output_collection name="out_cr" type="list" count="4"> - <element name="ecoli_1K_1.fastq.gz.fastq0_0.cor"> + <output_collection name="out_cr" type="list" count="2"> + <element name="ecoli_1K_1.fastq.gz.fastq0_0"> <assert_contents> <has_size value="34468" delta="2000"/> </assert_contents> </element> - <element name="ecoli_1K_2.fastq.gz.fastq0_0.cor"> + <element name="ecoli_1K_2.fastq.gz.fastq0_0"> <assert_contents> <has_size value="34468" delta="2000"/> </assert_contents>