From f637f04ab0e00cb84208c7bd891db429d6552c7e Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 29 Apr 2024 04:21:27 +0000 Subject: [PATCH 1/3] Updating tools/hapcut2 from version 1.3.3 to 1.3.4 --- tools/hapcut2/hapcut2.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/hapcut2/hapcut2.xml b/tools/hapcut2/hapcut2.xml index 9790c09e60d..e16e7817794 100644 --- a/tools/hapcut2/hapcut2.xml +++ b/tools/hapcut2/hapcut2.xml @@ -2,8 +2,8 @@ haplotype assembly for diploid organisms - 1.3.3 - 1 + 1.3.4 + 0 From 7328403dfd81edaa8776b5eb027de698b00f939b Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Mon, 29 Apr 2024 17:09:27 +0200 Subject: [PATCH 2/3] Version bump and restructuring of XML file --- tools/hapcut2/hapcut2.xml | 120 ++++++++++++-------------------------- tools/hapcut2/macros.xml | 24 ++++++++ 2 files changed, 62 insertions(+), 82 deletions(-) create mode 100644 tools/hapcut2/macros.xml diff --git a/tools/hapcut2/hapcut2.xml b/tools/hapcut2/hapcut2.xml index e16e7817794..cf97344a4c5 100644 --- a/tools/hapcut2/hapcut2.xml +++ b/tools/hapcut2/hapcut2.xml @@ -1,40 +1,16 @@ - + haplotype assembly for diploid organisms - 1.3.4 - 0 - - - - - - - - - - - - - - - - - - - + 1 + macros.xml - hapcut2 hapcut2 - - - - + + @@ -107,49 +67,31 @@ ln -s '$input_bam' input.bam - + - + - - + + - - + +
- - - + +
- - + + output_phased - + output_fragments @@ -161,7 +103,9 @@ ln -s '$input_bam' input.bam - + + + @@ -171,7 +115,9 @@ ln -s '$input_bam' input.bam - + + + @@ -183,7 +129,9 @@ ln -s '$input_bam' input.bam - + + + @@ -195,8 +143,12 @@ ln -s '$input_bam' input.bam - - + + + + + + @@ -212,8 +164,12 @@ ln -s '$input_bam' input.bam - - + + + + + + @@ -262,7 +218,7 @@ See `HapCUT2 on GitHib `_ for more detailed .. class:: infomark -Quickmerge was wrapped by the Galaxy Australia team. +HapCUT2 was wrapped by the Galaxy Australia team. ]]> diff --git a/tools/hapcut2/macros.xml b/tools/hapcut2/macros.xml new file mode 100644 index 00000000000..6b7400953eb --- /dev/null +++ b/tools/hapcut2/macros.xml @@ -0,0 +1,24 @@ + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file From 55df8a0517ccafe859440bf5009e058e25a03163 Mon Sep 17 00:00:00 2001 From: Saim Momin Date: Tue, 30 Apr 2024 10:10:29 +0200 Subject: [PATCH 3/3] Updated changes as per review --- tools/hapcut2/hapcut2.xml | 6 +----- tools/hapcut2/macros.xml | 6 ++++++ 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/tools/hapcut2/hapcut2.xml b/tools/hapcut2/hapcut2.xml index cf97344a4c5..16e1d879e18 100644 --- a/tools/hapcut2/hapcut2.xml +++ b/tools/hapcut2/hapcut2.xml @@ -215,13 +215,9 @@ Input data should reference a single diploid individual mapped to a reference ge See `HapCUT2 on GitHib `_ for more detailed information. - -.. class:: infomark - -HapCUT2 was wrapped by the Galaxy Australia team. - ]]> 10.1101/gr.213462.116 +
diff --git a/tools/hapcut2/macros.xml b/tools/hapcut2/macros.xml index 6b7400953eb..703448893da 100644 --- a/tools/hapcut2/macros.xml +++ b/tools/hapcut2/macros.xml @@ -21,4 +21,10 @@
+ + + + + + \ No newline at end of file