From 6ad64a151908313a3fc1f975b7c9832444db05d3 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 25 Sep 2024 15:59:13 +0200 Subject: [PATCH 1/9] linter fixes for snpeff - remove deprecated and redundant filter_options_attribute - add expect_num_outputs (and improve tests) --- tool_collections/snpeff/.lint_skip | 3 -- tool_collections/snpeff/snpEff.xml | 28 +++++++++++-------- tool_collections/snpeff/snpEff_create_db.xml | 10 +++---- .../snpeff/snpeff_get_chr_names.xml | 6 ---- 4 files changed, 22 insertions(+), 25 deletions(-) delete mode 100644 tool_collections/snpeff/.lint_skip diff --git a/tool_collections/snpeff/.lint_skip b/tool_collections/snpeff/.lint_skip deleted file mode 100644 index a505b27b40f..00000000000 --- a/tool_collections/snpeff/.lint_skip +++ /dev/null @@ -1,3 +0,0 @@ -InputsDataOptionsFilterAttribFiltersType -InputsDataOptionsFiltersRef -TestsExpectNumOutputs diff --git a/tool_collections/snpeff/snpEff.xml b/tool_collections/snpeff/snpEff.xml index d5823bd30ce..aa23c82ee21 100644 --- a/tool_collections/snpeff/snpEff.xml +++ b/tool_collections/snpeff/snpEff.xml @@ -159,9 +159,6 @@ - - - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"
@@ -181,9 +178,6 @@ - - - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@" @@ -364,30 +358,35 @@ - generate_stats == True + generate_stats - csvStats == True + csvStats - + - + + + + + + - + @@ -396,12 +395,19 @@ + + + + + + + - + @@ -135,7 +135,7 @@ - + @@ -146,7 +146,7 @@ - + @@ -158,7 +158,7 @@ - + @@ -170,7 +170,7 @@ - + diff --git a/tool_collections/snpeff/snpeff_get_chr_names.xml b/tool_collections/snpeff/snpeff_get_chr_names.xml index 4cda6ba53b2..a1f5c4fa903 100644 --- a/tool_collections/snpeff/snpeff_get_chr_names.xml +++ b/tool_collections/snpeff/snpeff_get_chr_names.xml @@ -50,9 +50,6 @@ This can only be used on databases in your history that were downloaded using the snpEff download tool. - - - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@" @@ -65,9 +62,6 @@ This can only be used on databases in your history that were created using the snpEff build tool. - - - value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@" From ee59db36cb5692d50a554d33f635418664806d43 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:23:25 +0000 Subject: [PATCH 2/9] Updating tools/gtdbtk from version 2.3.2 to 2.4.0 --- tools/gtdbtk/macros.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/gtdbtk/macros.xml b/tools/gtdbtk/macros.xml index 585aaedc6c7..ae9c0b4198d 100644 --- a/tools/gtdbtk/macros.xml +++ b/tools/gtdbtk/macros.xml @@ -1,6 +1,6 @@ - 2.3.2 - 5 + 2.4.0 + 0 22.05 From 3882daf66fbfc34e0c5dd4ddd3ee0fd04505e14a Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:46:48 +0000 Subject: [PATCH 3/9] Updating tools/sinto from version 0.9.0 to 0.10.1 --- tools/sinto/macros.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/sinto/macros.xml b/tools/sinto/macros.xml index 358101d62fc..7cc41deb024 100644 --- a/tools/sinto/macros.xml +++ b/tools/sinto/macros.xml @@ -1,7 +1,7 @@ - 0.9.0 - 1 + 0.10.1 + 0 From d69c7092f9e9d907eedb203ccc2f9ded67c2d90d Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:51:07 +0000 Subject: [PATCH 4/9] Updating tools/tn93 from version 1.0.6 to 1.0.14 --- tools/tn93/macros.xml | 2 +- tools/tn93/readreduce.xml | 2 +- tools/tn93/tn93.xml | 2 +- tools/tn93/tn93_cluster.xml | 2 +- tools/tn93/tn93_filter.xml | 4 ++-- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tools/tn93/macros.xml b/tools/tn93/macros.xml index 7eb3ccdd729..d87e4e6dc71 100644 --- a/tools/tn93/macros.xml +++ b/tools/tn93/macros.xml @@ -1,6 +1,6 @@ - 1.0.6 + 1.0.14 tn93 diff --git a/tools/tn93/readreduce.xml b/tools/tn93/readreduce.xml index 02ab45deec9..d999f20bc2d 100644 --- a/tools/tn93/readreduce.xml +++ b/tools/tn93/readreduce.xml @@ -1,4 +1,4 @@ - + into clusters with TN-93 macros.xml diff --git a/tools/tn93/tn93.xml b/tools/tn93/tn93.xml index c52c902452c..46b2670da2f 100644 --- a/tools/tn93/tn93.xml +++ b/tools/tn93/tn93.xml @@ -1,4 +1,4 @@ - + compute distances between aligned sequences macros.xml diff --git a/tools/tn93/tn93_cluster.xml b/tools/tn93/tn93_cluster.xml index ee0e3329378..d91a60fb957 100755 --- a/tools/tn93/tn93_cluster.xml +++ b/tools/tn93/tn93_cluster.xml @@ -1,4 +1,4 @@ - + sequences that lie within a specific distance of each other macros.xml diff --git a/tools/tn93/tn93_filter.xml b/tools/tn93/tn93_filter.xml index dad9eb6d0fd..bd8fb1cd074 100755 --- a/tools/tn93/tn93_filter.xml +++ b/tools/tn93/tn93_filter.xml @@ -1,10 +1,10 @@ - + - remove sequences from a reference that are within a given distance of of a cluster macros.xml - biopython + biopython Date: Thu, 26 Sep 2024 12:52:43 +0000 Subject: [PATCH 5/9] Updating tools/tximport from version 1.22.0 to 1.30.0 --- tools/tximport/tximport.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/tximport/tximport.xml b/tools/tximport/tximport.xml index 06d2b2f0e52..e488ceff77a 100644 --- a/tools/tximport/tximport.xml +++ b/tools/tximport/tximport.xml @@ -1,6 +1,6 @@ - 1.22.0 + 1.30.0 Summarize transcript-level estimates for gene-level analysis @@ -9,8 +9,8 @@ bioconductor-tximport - bioconductor-genomicfeatures - r-getopt + bioconductor-genomicfeatures + r-getopt From 2450491ccbecc9e77bb9bb394a0e9205c54139b9 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:52:48 +0000 Subject: [PATCH 6/9] Updating tools/ucsc_blat from version 377 to 469 --- tools/ucsc_blat/blat.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/ucsc_blat/blat.xml b/tools/ucsc_blat/blat.xml index ca495760500..3d9ba5f669d 100644 --- a/tools/ucsc_blat/blat.xml +++ b/tools/ucsc_blat/blat.xml @@ -1,8 +1,8 @@ BLAST-like sequence alignment tool - 377 - 2 + 469 + 0 From 20bb4574009201d7be336d6a572cad10eed8e74d Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:53:09 +0000 Subject: [PATCH 7/9] Updating tools/ucsc_tools/ucsc_chainsort from version 455 to 469 --- tools/ucsc_tools/ucsc_chainsort/chainsort.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/ucsc_tools/ucsc_chainsort/chainsort.xml b/tools/ucsc_tools/ucsc_chainsort/chainsort.xml index 6ad56cd047b..eb84c1b71f3 100644 --- a/tools/ucsc_tools/ucsc_chainsort/chainsort.xml +++ b/tools/ucsc_tools/ucsc_chainsort/chainsort.xml @@ -3,7 +3,7 @@ Sort chains - 455 + 469 UCSC_Genome_Browser_Utilities From 5b2d50a92a7d4274acd2366ec2210e7cf2302b96 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Thu, 26 Sep 2024 12:53:45 +0000 Subject: [PATCH 8/9] Updating tools/umi_tools from version 1.1.2 to 1.1.5 --- tools/umi_tools/macros.xml | 4 ++-- tools/umi_tools/umi-tools_dedup.xml | 2 +- tools/umi_tools/umi-tools_group.xml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/umi_tools/macros.xml b/tools/umi_tools/macros.xml index f8db2fac1f8..7b3ae415140 100644 --- a/tools/umi_tools/macros.xml +++ b/tools/umi_tools/macros.xml @@ -3,8 +3,8 @@ - 1.1.2 - 2 + 1.1.5 + 0 21.01 diff --git a/tools/umi_tools/umi-tools_dedup.xml b/tools/umi_tools/umi-tools_dedup.xml index a0515ecc75e..70f4cfecc54 100644 --- a/tools/umi_tools/umi-tools_dedup.xml +++ b/tools/umi_tools/umi-tools_dedup.xml @@ -5,7 +5,7 @@ macros.xml - samtools + samtools macros.xml - samtools + samtools Date: Thu, 26 Sep 2024 15:22:59 +0200 Subject: [PATCH 9/9] Change expected db version --- tools/gtdbtk/gtdbtk_classify_wf.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/gtdbtk/gtdbtk_classify_wf.xml b/tools/gtdbtk/gtdbtk_classify_wf.xml index b9b0f7e6382..88c9fcae64b 100644 --- a/tools/gtdbtk/gtdbtk_classify_wf.xml +++ b/tools/gtdbtk/gtdbtk_classify_wf.xml @@ -39,7 +39,7 @@ $advanced.force - +