From 4c139b058eedf0155f6e8842d67b14cf6bde70ec Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Wed, 4 Sep 2024 11:59:10 +0200 Subject: [PATCH 1/4] fix urls, the folder has now underscore --- tools/ucsc_tools/fasplit/.shed.yml | 2 +- tools/ucsc_tools/fatovcf/.shed.yml | 2 +- tools/ucsc_tools/maftoaxt/.shed.yml | 2 +- tools/ucsc_tools/twobittofa/.shed.yml | 2 +- tools/ucsc_tools/ucsc_axtchain/.shed.yml | 2 +- tools/ucsc_tools/ucsc_axttomaf/.shed.yml | 2 +- tools/ucsc_tools/ucsc_chainnet/.shed.yml | 2 +- tools/ucsc_tools/ucsc_chainprenet/.shed.yml | 2 +- tools/ucsc_tools/ucsc_chainsort/.shed.yml | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/tools/ucsc_tools/fasplit/.shed.yml b/tools/ucsc_tools/fasplit/.shed.yml index 537b99c632c..25d6e998d9a 100644 --- a/tools/ucsc_tools/fasplit/.shed.yml +++ b/tools/ucsc_tools/fasplit/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: faSplit is a tool to split a single FASTA file into several files long_description: faSplit is a tool to split a single FASTA file into several files homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit type: unrestricted categories: - Fasta Manipulation diff --git a/tools/ucsc_tools/fatovcf/.shed.yml b/tools/ucsc_tools/fatovcf/.shed.yml index 0d7adf026ac..4fba9dbca7d 100644 --- a/tools/ucsc_tools/fatovcf/.shed.yml +++ b/tools/ucsc_tools/fatovcf/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ long_description: Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs by comparing the given FASTA sequences with a selectable reference. In default setting the first entry of the FASTA alignment file will serve as a reference. -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf type: unrestricted categories: - Convert Formats diff --git a/tools/ucsc_tools/maftoaxt/.shed.yml b/tools/ucsc_tools/maftoaxt/.shed.yml index 0481031d8ec..793cc832c2b 100644 --- a/tools/ucsc_tools/maftoaxt/.shed.yml +++ b/tools/ucsc_tools/maftoaxt/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: Convert dataset from MAF to axt format long_description: Convert MAF dataset to axt format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction. homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/maftoaxt +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt type: unrestricted categories: - Convert Formats diff --git a/tools/ucsc_tools/twobittofa/.shed.yml b/tools/ucsc_tools/twobittofa/.shed.yml index 43bd19a4fdb..e1d6443f3f9 100644 --- a/tools/ucsc_tools/twobittofa/.shed.yml +++ b/tools/ucsc_tools/twobittofa/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: twoBitToFa is a tool to convert all or part of .2bit file to FASTA long_description: twoBitToFa is a tool to convert all or part of .2bit file to FASTA homepage_url: https://genome.ucsc.edu/goldenpath/help/twoBit.html -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa type: unrestricted categories: - Convert Formats diff --git a/tools/ucsc_tools/ucsc_axtchain/.shed.yml b/tools/ucsc_tools/ucsc_axtchain/.shed.yml index 30db97c43be..2dd1f5d7e59 100644 --- a/tools/ucsc_tools/ucsc_axtchain/.shed.yml +++ b/tools/ucsc_tools/ucsc_axtchain/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: Chain together genome alignments long_description: Create a chain file from a genome alignment. The chain format describes a pairwise alignment that allow gaps in both sequences simultaneously. homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axtchain +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axtchain type: unrestricted categories: - Sequence Analysis diff --git a/tools/ucsc_tools/ucsc_axttomaf/.shed.yml b/tools/ucsc_tools/ucsc_axttomaf/.shed.yml index 06f89575b5c..24e2d858785 100644 --- a/tools/ucsc_tools/ucsc_axttomaf/.shed.yml +++ b/tools/ucsc_tools/ucsc_axttomaf/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: Convert dataset from axt to MAF format. long_description: This is a tool from the UCSC suite to convert dataset from axt to MAF format. homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/axttomaf +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/axttomaf type: unrestricted categories: - Convert Formats diff --git a/tools/ucsc_tools/ucsc_chainnet/.shed.yml b/tools/ucsc_tools/ucsc_chainnet/.shed.yml index 8cb2e1d503d..5bd38595cc0 100644 --- a/tools/ucsc_tools/ucsc_chainnet/.shed.yml +++ b/tools/ucsc_tools/ucsc_chainnet/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: Make alignment nets out of chains long_description: homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/ucsc_chainnet +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet type: unrestricted categories: - Sequence Analysis diff --git a/tools/ucsc_tools/ucsc_chainprenet/.shed.yml b/tools/ucsc_tools/ucsc_chainprenet/.shed.yml index e639367352b..e54838d81eb 100644 --- a/tools/ucsc_tools/ucsc_chainprenet/.shed.yml +++ b/tools/ucsc_tools/ucsc_chainprenet/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: Remove chains that don't have a chance of being netted long_description: Some chains can't be converted to a net, this tool filters them out. Part of the UCSC genome browser utilities to work with the chain format. homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainprenet +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainprenet type: unrestricted categories: - Sequence Analysis diff --git a/tools/ucsc_tools/ucsc_chainsort/.shed.yml b/tools/ucsc_tools/ucsc_chainsort/.shed.yml index 0e268a8518b..5855bb3eec7 100644 --- a/tools/ucsc_tools/ucsc_chainsort/.shed.yml +++ b/tools/ucsc_tools/ucsc_chainsort/.shed.yml @@ -3,7 +3,7 @@ owner: iuc description: Sort chains. By default sorts by score. long_description: Note this loads all chains into memory, so it is not suitable for large sets. Instead, run chainSort on multiple small files, followed by chainMergeSort. homepage_url: http://hgdownload.cse.ucsc.edu/admin/exe/ -remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/chainsort +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/chainsort type: unrestricted categories: - Sequence Analysis From d6f698dc8c8614c9aee7aa223d49e94ed48e44ad Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 19 Sep 2024 17:21:52 +0200 Subject: [PATCH 2/4] update and polish ucsc/kent tools --- tools/ucsc_tools/fasplit/.lint_skip | 2 -- tools/ucsc_tools/fasplit/fasplit.xml | 14 +++++++++----- tools/ucsc_tools/fatovcf/fatovcf.xml | 10 +++++++--- tools/ucsc_tools/maftoaxt/maftoaxt.xml | 11 ++++++++--- tools/ucsc_tools/twobittofa/.lint_skip | 2 -- tools/ucsc_tools/twobittofa/twobittofa.xml | 14 ++++++++++---- tools/ucsc_tools/ucsc_axtchain/axtchain.xml | 7 +++++-- tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml | 5 ++++- tools/ucsc_tools/ucsc_chainprenet/chainprenet.xml | 9 +++++++-- tools/ucsc_tools/ucsc_chainsort/chainsort.xml | 8 ++++++-- tools/ucsc_tools/ucsc_netfilter/netfilter.xml | 6 +++++- tools/ucsc_tools/ucsc_netsyntenic/netsyntenic.xml | 5 ++++- tools/ucsc_tools/wigtobigwig/wigtobigwig.xml | 11 +++++++---- 13 files changed, 72 insertions(+), 32 deletions(-) delete mode 100644 tools/ucsc_tools/fasplit/.lint_skip delete mode 100644 tools/ucsc_tools/twobittofa/.lint_skip diff --git a/tools/ucsc_tools/fasplit/.lint_skip b/tools/ucsc_tools/fasplit/.lint_skip deleted file mode 100644 index af4cf5ec3d4..00000000000 --- a/tools/ucsc_tools/fasplit/.lint_skip +++ /dev/null @@ -1,2 +0,0 @@ -CitationsNoValid -XMLOrder diff --git a/tools/ucsc_tools/fasplit/fasplit.xml b/tools/ucsc_tools/fasplit/fasplit.xml index 0fccfed9dbd..3d0517f320a 100644 --- a/tools/ucsc_tools/fasplit/fasplit.xml +++ b/tools/ucsc_tools/fasplit/fasplit.xml @@ -1,11 +1,11 @@ Split a FASTA file + + 469 + UCSC_Genome_Browser_Utilities - - 377 - ucsc-fasplit @@ -57,7 +57,7 @@ out/ - + @@ -102,7 +102,7 @@ out/ - + + 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/fatovcf/fatovcf.xml b/tools/ucsc_tools/fatovcf/fatovcf.xml index e9cc183f587..acf9bf009ef 100644 --- a/tools/ucsc_tools/fatovcf/fatovcf.xml +++ b/tools/ucsc_tools/fatovcf/fatovcf.xml @@ -48,7 +48,7 @@ ]]> - + @@ -76,7 +76,7 @@ - + @@ -136,7 +136,11 @@ `faToVcf`_ is a tool to extract a VCF from a multi-sequence FASTA alignment. -.. _faToVcf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +For implementation details see faToVcf's `source code`_. + +.. _faToVcf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/faToVcf/faToVcf.c + ]]> 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/maftoaxt/maftoaxt.xml b/tools/ucsc_tools/maftoaxt/maftoaxt.xml index c4273f45ab4..2f746068c9d 100644 --- a/tools/ucsc_tools/maftoaxt/maftoaxt.xml +++ b/tools/ucsc_tools/maftoaxt/maftoaxt.xml @@ -3,7 +3,7 @@ Convert file from MAF to axt format - 377 + 469 UCSC_Genome_Browser_Utilities @@ -25,7 +25,7 @@ $stripDb ]]> - + @@ -62,9 +62,14 @@ 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/twobittofa/.lint_skip b/tools/ucsc_tools/twobittofa/.lint_skip deleted file mode 100644 index af4cf5ec3d4..00000000000 --- a/tools/ucsc_tools/twobittofa/.lint_skip +++ /dev/null @@ -1,2 +0,0 @@ -CitationsNoValid -XMLOrder diff --git a/tools/ucsc_tools/twobittofa/twobittofa.xml b/tools/ucsc_tools/twobittofa/twobittofa.xml index 81de4fddd71..7c73b96dbf3 100644 --- a/tools/ucsc_tools/twobittofa/twobittofa.xml +++ b/tools/ucsc_tools/twobittofa/twobittofa.xml @@ -1,11 +1,11 @@ Convert all or part of .2bit file to FASTA + + 469 + UCSC_Genome_Browser_Utilities - - 377 - ucsc-twobittofa @@ -57,10 +57,16 @@ $noMask `_. + +For implementation details see twoBitToFa's `source code`_. + +.. _twoBitToFa: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/twoBitToFa/twoBitToFa.c ]]> + 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/ucsc_axtchain/axtchain.xml b/tools/ucsc_tools/ucsc_axtchain/axtchain.xml index 63c0ab0adbf..ebcf2c838fd 100644 --- a/tools/ucsc_tools/ucsc_axtchain/axtchain.xml +++ b/tools/ucsc_tools/ucsc_axtchain/axtchain.xml @@ -3,7 +3,7 @@ Chain together axt alignments - 455 + 469 UCSC_Genome_Browser_Utilities @@ -70,7 +70,7 @@ 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml b/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml index ec60e2659af..fffe3758e92 100644 --- a/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml +++ b/tools/ucsc_tools/ucsc_axttomaf/axttomaf.xml @@ -3,7 +3,7 @@ Convert dataset from axt to MAF format - 377 + 469 UCSC_Genome_Browser_Utilities @@ -95,9 +95,12 @@ `axtToMaf`_ is a tool to convert dataset from `axt format`_ to `MAF format`_. +For implementation details see axtToMaf's `source code`_. + .. _axtToMaf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt .. _axt format: https://genome.ucsc.edu/goldenPath/help/axt.html .. _MAF format: https://genome.ucsc.edu/FAQ/FAQformat.html#format5 +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/axtToMaf/axtToMaf.c ]]> 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/ucsc_chainprenet/chainprenet.xml b/tools/ucsc_tools/ucsc_chainprenet/chainprenet.xml index 0b82d597e8b..046719b051b 100644 --- a/tools/ucsc_tools/ucsc_chainprenet/chainprenet.xml +++ b/tools/ucsc_tools/ucsc_chainprenet/chainprenet.xml @@ -3,7 +3,7 @@ Remove chains that don't have a chance of being netted - 377 + 469 UCSC_Genome_Browser_Utilities @@ -102,9 +102,14 @@ 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/ucsc_chainsort/chainsort.xml b/tools/ucsc_tools/ucsc_chainsort/chainsort.xml index 0e9150572ba..6ad56cd047b 100644 --- a/tools/ucsc_tools/ucsc_chainsort/chainsort.xml +++ b/tools/ucsc_tools/ucsc_chainsort/chainsort.xml @@ -43,12 +43,16 @@ +.. _chains: https://genome.ucsc.edu/goldenPath/help/chain.html +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/chainSort/chainSort.c +]]> 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/ucsc_netfilter/netfilter.xml b/tools/ucsc_tools/ucsc_netfilter/netfilter.xml index cbcba2d6f97..f220f333627 100644 --- a/tools/ucsc_tools/ucsc_netfilter/netfilter.xml +++ b/tools/ucsc_tools/ucsc_netfilter/netfilter.xml @@ -72,9 +72,13 @@ 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/ucsc_netsyntenic/netsyntenic.xml b/tools/ucsc_tools/ucsc_netsyntenic/netsyntenic.xml index abdbf6faae7..e073b7dbf36 100644 --- a/tools/ucsc_tools/ucsc_netsyntenic/netsyntenic.xml +++ b/tools/ucsc_tools/ucsc_netsyntenic/netsyntenic.xml @@ -32,10 +32,13 @@ 10.1093/bib/bbs038 diff --git a/tools/ucsc_tools/wigtobigwig/wigtobigwig.xml b/tools/ucsc_tools/wigtobigwig/wigtobigwig.xml index 05f66e0eb30..fb54054d82e 100644 --- a/tools/ucsc_tools/wigtobigwig/wigtobigwig.xml +++ b/tools/ucsc_tools/wigtobigwig/wigtobigwig.xml @@ -1,7 +1,7 @@ bedGraph or Wig to bigWig converter - 447 + 469 UCSC_Genome_Browser_Utilities @@ -134,7 +134,7 @@ - + +.. _UCSC Bioinformatics website: http://genome.ucsc.edu/goldenPath/help/bedgraph.html +.. _docs: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt +.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/utils/wigToBigWig/wigToBigWig.c +]]> 10.1093/bioinformatics/btq351 From 6f60c0b709165d28b09cf3dda542edd36adf6932 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 19 Sep 2024 21:19:07 +0200 Subject: [PATCH 3/4] add missing profiles --- tools/ucsc_tools/fasplit/fasplit.xml | 2 +- tools/ucsc_tools/twobittofa/twobittofa.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/ucsc_tools/fasplit/fasplit.xml b/tools/ucsc_tools/fasplit/fasplit.xml index 3d0517f320a..a2282c48f68 100644 --- a/tools/ucsc_tools/fasplit/fasplit.xml +++ b/tools/ucsc_tools/fasplit/fasplit.xml @@ -1,4 +1,4 @@ - + Split a FASTA file 469 diff --git a/tools/ucsc_tools/twobittofa/twobittofa.xml b/tools/ucsc_tools/twobittofa/twobittofa.xml index 7c73b96dbf3..67cca4ec671 100644 --- a/tools/ucsc_tools/twobittofa/twobittofa.xml +++ b/tools/ucsc_tools/twobittofa/twobittofa.xml @@ -1,4 +1,4 @@ - + Convert all or part of .2bit file to FASTA 469 From 17811e992ecb5b8491444b95c944fd9f9b64e440 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 20 Sep 2024 08:42:20 +0200 Subject: [PATCH 4/4] order output collection elements newer profile expects that --- tools/ucsc_tools/fasplit/fasplit.xml | 48 ++++++++++++++-------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/tools/ucsc_tools/fasplit/fasplit.xml b/tools/ucsc_tools/fasplit/fasplit.xml index a2282c48f68..b86ffcf4a46 100644 --- a/tools/ucsc_tools/fasplit/fasplit.xml +++ b/tools/ucsc_tools/fasplit/fasplit.xml @@ -64,43 +64,43 @@ out/ - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + +