| Previous changeset 21:a789e163a670 (2022-08-10) Next changeset 23:a90db5dbaaf3 (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 spades.xml |
| b |
| diff -r a789e163a670 -r 33368fec3b70 macros.xml --- a/macros.xml Wed Aug 10 13:13:59 2022 +0000 +++ b/macros.xml Tue Aug 23 07:58:51 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"> |
| b |
| diff -r a789e163a670 -r 33368fec3b70 spades.xml --- a/spades.xml Wed Aug 10 13:13:59 2022 +0000 +++ b/spades.xml Tue Aug 23 07:58:51 2022 +0000 |
| b |
| @@ -312,17 +312,17 @@ <param name="mode_sel" value="--careful"/> <param name="optional_output" value="cr,l"/> <output_collection name="out_cr" type="list" count="3"> - <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_1.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <assert_contents> <has_size value="20" delta="5"/> </assert_contents> @@ -344,17 +344,17 @@ <param name="mode_sel" value="--careful,--sc"/> <param name="optional_output" value="cr,l"/> <output_collection name="out_cr" type="list" count="3"> - <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_1.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <assert_contents> <has_size value="20" delta="5"/> </assert_contents> @@ -408,17 +408,17 @@ </conditional> <param name="optional_output" value="cr,l"/> <output_collection name="out_cr" type="list" count="3"> - <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_1.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <assert_contents> <has_size value="20" delta="5"/> </assert_contents> @@ -440,17 +440,17 @@ <param name="mode_sel" value="--sc"/> <param name="optional_output" value="cr,l"/> <output_collection name="out_cr" type="list" count="3"> - <element name="ecoli_1K.fastq.gz_1.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_1.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz_2.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz_2.00.0_0"> <assert_contents> <has_size value="130317" delta="5000"/> </assert_contents> </element> - <element name="ecoli_1K.fastq.gz__unpaired.00.0_0.cor"> + <element name="ecoli_1K.fastq.gz__unpaired.00.0_0"> <assert_contents> <has_size value="20" delta="5"/> </assert_contents> |