| Previous changeset 6:75405f5e2cc5 (2022-08-10) Next changeset 8:7bb235ff0746 (2024-02-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 69c6e337e239e84ce8fec9cf9fb5d820136877b2 |
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modified:
macros.xml plasmidspades.xml |
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| diff -r 75405f5e2cc5 -r 1708851f8804 macros.xml --- a/macros.xml Wed Aug 10 13:15:28 2022 +0000 +++ b/macros.xml Tue Aug 23 08:00:05 2022 +0000 |
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| @@ -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"> |
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| diff -r 75405f5e2cc5 -r 1708851f8804 plasmidspades.xml --- a/plasmidspades.xml Wed Aug 10 13:15:28 2022 +0000 +++ b/plasmidspades.xml Tue Aug 23 08:00:05 2022 +0000 |
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| @@ -162,17 +162,17 @@ </assert_contents> </output> <output_collection name="out_cr" type="list" count="3"> - <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <element name="pl1.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <element name="pl2.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl_unpaired.00.0_0.cor"> + <element name="pl_unpaired.00.0_0"> <assert_contents> <has_size value="392" delta="100"/> </assert_contents> @@ -251,17 +251,17 @@ </conditional> <param name="optional_output" value="cr,l"/> <output_collection name="out_cr" type="list" count="3"> - <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <element name="pl1.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <element name="pl2.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl_unpaired.00.0_0.cor"> + <element name="pl_unpaired.00.0_0"> <assert_contents> <has_size value="392" delta="100"/> </assert_contents> @@ -283,17 +283,17 @@ </conditional> <param name="optional_output" value="cr,l"/> <output_collection name="out_cr" type="list" count="3"> - <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <element name="pl1.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <element name="pl2.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl_unpaired.00.0_0.cor"> + <element name="pl_unpaired.00.0_0"> <assert_contents> <has_size value="392" delta="100"/> </assert_contents> @@ -327,17 +327,17 @@ <param name="mode_sel" value="--careful"/> <param name="optional_output" value="cr,l"/> <output_collection name="out_cr" type="list" count="3"> - <element name="pl1.fq.gz.fastq.00.0_0.cor"> + <element name="pl1.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl2.fq.gz.fastq.00.0_0.cor"> + <element name="pl2.fq.gz.fastq.00.0_0"> <assert_contents> <has_size value="72173" delta="1000"/> </assert_contents> </element> - <element name="pl_unpaired.00.0_0.cor"> + <element name="pl_unpaired.00.0_0"> <assert_contents> <has_size value="392" delta="100"/> </assert_contents> |