diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 93f9a050..6294c535 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -14,7 +14,7 @@ on:
- '*'
env:
GALAXY_FORK: galaxyproject
- GALAXY_BRANCH: release_23.2
+ GALAXY_BRANCH: release_23.1
MAX_CHUNKS: 4
MAX_FILE_SIZE: 2M
concurrency:
diff --git a/tools/wisecondorx/.shed.yml b/tools/wisecondorx/.shed.yml
new file mode 100644
index 00000000..b86281f5
--- /dev/null
+++ b/tools/wisecondorx/.shed.yml
@@ -0,0 +1,13 @@
+# .shed.yml supporting automatic pushes.
+owner: artbio
+name: wisecondorx
+description: WisecondorX
+long_description: |
+ Improved copy number detection for routine shallow whole-genome sequencing.
+ See homepage URL for manual and code.
+categories:
+ - Variant Analysis
+homepage_url: https://github.com/CenterForMedicalGeneticsGhent/WisecondorX/tree/master
+remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/master/tools/wisecondorx
+toolshed:
+ - toolshed
diff --git a/tools/wisecondorx/macro.xml b/tools/wisecondorx/macro.xml
new file mode 100644
index 00000000..d809f705
--- /dev/null
+++ b/tools/wisecondorx/macro.xml
@@ -0,0 +1,54 @@
+
+ 1.2.9
+ @VERSION@+galaxy0
+ 23.0
+
+
+
+
+ wisecondorx
+
+
+
+
diff --git a/tools/wisecondorx/test-data/0.ref.npz b/tools/wisecondorx/test-data/0.ref.npz
new file mode 100644
index 00000000..c44bc56f
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index 00000000..b8dec4a9
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diff --git a/tools/wisecondorx/test-data/2.ref.npz b/tools/wisecondorx/test-data/2.ref.npz
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index 00000000..36c8285c
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diff --git a/tools/wisecondorx/test-data/3.ref.npz b/tools/wisecondorx/test-data/3.ref.npz
new file mode 100644
index 00000000..c87a57a8
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diff --git a/tools/wisecondorx/test-data/4.ref.npz b/tools/wisecondorx/test-data/4.ref.npz
new file mode 100644
index 00000000..e2f25644
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diff --git a/tools/wisecondorx/test-data/5.ref.npz b/tools/wisecondorx/test-data/5.ref.npz
new file mode 100644
index 00000000..299af5d5
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diff --git a/tools/wisecondorx/test-data/6.ref.npz b/tools/wisecondorx/test-data/6.ref.npz
new file mode 100644
index 00000000..1629ccd8
Binary files /dev/null and b/tools/wisecondorx/test-data/6.ref.npz differ
diff --git a/tools/wisecondorx/test-data/7.ref.npz b/tools/wisecondorx/test-data/7.ref.npz
new file mode 100644
index 00000000..05433e37
Binary files /dev/null and b/tools/wisecondorx/test-data/7.ref.npz differ
diff --git a/tools/wisecondorx/test-data/8.ref.npz b/tools/wisecondorx/test-data/8.ref.npz
new file mode 100644
index 00000000..ac436a88
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diff --git a/tools/wisecondorx/test-data/9.ref.npz b/tools/wisecondorx/test-data/9.ref.npz
new file mode 100644
index 00000000..a999bca2
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diff --git a/tools/wisecondorx/test-data/chr1.png b/tools/wisecondorx/test-data/chr1.png
new file mode 100644
index 00000000..ca4527e9
Binary files /dev/null and b/tools/wisecondorx/test-data/chr1.png differ
diff --git a/tools/wisecondorx/test-data/chr10.png b/tools/wisecondorx/test-data/chr10.png
new file mode 100644
index 00000000..96771ef0
Binary files /dev/null and b/tools/wisecondorx/test-data/chr10.png differ
diff --git a/tools/wisecondorx/test-data/chr11.png b/tools/wisecondorx/test-data/chr11.png
new file mode 100644
index 00000000..a4b49547
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diff --git a/tools/wisecondorx/test-data/chr12.png b/tools/wisecondorx/test-data/chr12.png
new file mode 100644
index 00000000..59c5cf9f
Binary files /dev/null and b/tools/wisecondorx/test-data/chr12.png differ
diff --git a/tools/wisecondorx/test-data/chr13.png b/tools/wisecondorx/test-data/chr13.png
new file mode 100644
index 00000000..91272a96
Binary files /dev/null and b/tools/wisecondorx/test-data/chr13.png differ
diff --git a/tools/wisecondorx/test-data/chr14.png b/tools/wisecondorx/test-data/chr14.png
new file mode 100644
index 00000000..88cb149a
Binary files /dev/null and b/tools/wisecondorx/test-data/chr14.png differ
diff --git a/tools/wisecondorx/test-data/chr15.png b/tools/wisecondorx/test-data/chr15.png
new file mode 100644
index 00000000..381a4a70
Binary files /dev/null and b/tools/wisecondorx/test-data/chr15.png differ
diff --git a/tools/wisecondorx/test-data/chr16.png b/tools/wisecondorx/test-data/chr16.png
new file mode 100644
index 00000000..92524e8b
Binary files /dev/null and b/tools/wisecondorx/test-data/chr16.png differ
diff --git a/tools/wisecondorx/test-data/chr17.png b/tools/wisecondorx/test-data/chr17.png
new file mode 100644
index 00000000..f57b5da7
Binary files /dev/null and b/tools/wisecondorx/test-data/chr17.png differ
diff --git a/tools/wisecondorx/test-data/chr18.png b/tools/wisecondorx/test-data/chr18.png
new file mode 100644
index 00000000..6e5038d2
Binary files /dev/null and b/tools/wisecondorx/test-data/chr18.png differ
diff --git a/tools/wisecondorx/test-data/chr19.png b/tools/wisecondorx/test-data/chr19.png
new file mode 100644
index 00000000..a5f27c27
Binary files /dev/null and b/tools/wisecondorx/test-data/chr19.png differ
diff --git a/tools/wisecondorx/test-data/chr2.png b/tools/wisecondorx/test-data/chr2.png
new file mode 100644
index 00000000..85d467f0
Binary files /dev/null and b/tools/wisecondorx/test-data/chr2.png differ
diff --git a/tools/wisecondorx/test-data/chr20.png b/tools/wisecondorx/test-data/chr20.png
new file mode 100644
index 00000000..3c6b0ba9
Binary files /dev/null and b/tools/wisecondorx/test-data/chr20.png differ
diff --git a/tools/wisecondorx/test-data/chr21.png b/tools/wisecondorx/test-data/chr21.png
new file mode 100644
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diff --git a/tools/wisecondorx/test-data/chr22.png b/tools/wisecondorx/test-data/chr22.png
new file mode 100644
index 00000000..4ef80912
Binary files /dev/null and b/tools/wisecondorx/test-data/chr22.png differ
diff --git a/tools/wisecondorx/test-data/chr3.png b/tools/wisecondorx/test-data/chr3.png
new file mode 100644
index 00000000..49453db2
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diff --git a/tools/wisecondorx/test-data/chr4.png b/tools/wisecondorx/test-data/chr4.png
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new file mode 100644
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Binary files /dev/null and b/tools/wisecondorx/test-data/chr5.png differ
diff --git a/tools/wisecondorx/test-data/chr6.png b/tools/wisecondorx/test-data/chr6.png
new file mode 100644
index 00000000..6d0b90ba
Binary files /dev/null and b/tools/wisecondorx/test-data/chr6.png differ
diff --git a/tools/wisecondorx/test-data/chr7.png b/tools/wisecondorx/test-data/chr7.png
new file mode 100644
index 00000000..934f2906
Binary files /dev/null and b/tools/wisecondorx/test-data/chr7.png differ
diff --git a/tools/wisecondorx/test-data/chr8.png b/tools/wisecondorx/test-data/chr8.png
new file mode 100644
index 00000000..65f43a35
Binary files /dev/null and b/tools/wisecondorx/test-data/chr8.png differ
diff --git a/tools/wisecondorx/test-data/chr9.png b/tools/wisecondorx/test-data/chr9.png
new file mode 100644
index 00000000..98c0a568
Binary files /dev/null and b/tools/wisecondorx/test-data/chr9.png differ
diff --git a/tools/wisecondorx/test-data/chrX.png b/tools/wisecondorx/test-data/chrX.png
new file mode 100644
index 00000000..729331b7
Binary files /dev/null and b/tools/wisecondorx/test-data/chrX.png differ
diff --git a/tools/wisecondorx/test-data/genome_wide.png b/tools/wisecondorx/test-data/genome_wide.png
new file mode 100644
index 00000000..9e4bfbc3
Binary files /dev/null and b/tools/wisecondorx/test-data/genome_wide.png differ
diff --git a/tools/wisecondorx/test-data/input_reference_predict.10000kb.npz b/tools/wisecondorx/test-data/input_reference_predict.10000kb.npz
new file mode 100644
index 00000000..937eba46
Binary files /dev/null and b/tools/wisecondorx/test-data/input_reference_predict.10000kb.npz differ
diff --git a/tools/wisecondorx/test-data/input_sample_predict.npz b/tools/wisecondorx/test-data/input_sample_predict.npz
new file mode 100644
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Binary files /dev/null and b/tools/wisecondorx/test-data/input_sample_predict.npz differ
diff --git a/tools/wisecondorx/test-data/npz_convert_input.bam b/tools/wisecondorx/test-data/npz_convert_input.bam
new file mode 100644
index 00000000..f1b990dc
Binary files /dev/null and b/tools/wisecondorx/test-data/npz_convert_input.bam differ
diff --git a/tools/wisecondorx/test-data/npz_convert_output.npz b/tools/wisecondorx/test-data/npz_convert_output.npz
new file mode 100644
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Binary files /dev/null and b/tools/wisecondorx/test-data/npz_convert_output.npz differ
diff --git a/tools/wisecondorx/test-data/output_reference.npz b/tools/wisecondorx/test-data/output_reference.npz
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diff --git a/tools/wisecondorx/test-data/predict_abberations.bed b/tools/wisecondorx/test-data/predict_abberations.bed
new file mode 100644
index 00000000..2d3f5623
--- /dev/null
+++ b/tools/wisecondorx/test-data/predict_abberations.bed
@@ -0,0 +1 @@
+chr start end ratio zscore type
diff --git a/tools/wisecondorx/test-data/predict_bins.bed b/tools/wisecondorx/test-data/predict_bins.bed
new file mode 100644
index 00000000..b4e98937
--- /dev/null
+++ b/tools/wisecondorx/test-data/predict_bins.bed
@@ -0,0 +1,317 @@
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diff --git a/tools/wisecondorx/test-data/predict_segments.bed b/tools/wisecondorx/test-data/predict_segments.bed
new file mode 100644
index 00000000..1ab2f97d
--- /dev/null
+++ b/tools/wisecondorx/test-data/predict_segments.bed
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diff --git a/tools/wisecondorx/test-data/predict_statistics.txt b/tools/wisecondorx/test-data/predict_statistics.txt
new file mode 100644
index 00000000..901e11f9
--- /dev/null
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+11 -0.0010682214397647377 -0.012687471128064745 -0.25403103304752794
+12 -0.006720586939014568 -0.007785953193232591 -1.7313975674091997
+13 0.009139617144346813 0.002351198145606662 2.7174009747784944
+14 0.004617644740226149 0.0035058727944338825 1.4966978929197126
+15 0.0021565565774295426 -0.005083704704282363 0.5800013406347537
+16 0.0009244703405124733 0.007301717962691849 0.20870556732386122
+17 0.01982791519920036 0.006869817773389827 3.1146698354398854
+18 0.020898589066626748 0.009665993221586318 2.845910113450034
+19 -0.000657740980105667 0.0016192329112033454 -0.08006761423301532
+20 0.003446546608787667 0.002058925822068644 0.5033887759993748
+21 -0.005290652555760193 -0.011028957124213846 -0.5341417465937656
+22 -0.017713587100928845 -0.0327155577009055 -1.6790692284983704
+X -0.013378674115274611 -0.015072799437654107 -2.6107602961602137
+Gender based on --yfrac (or manually overridden by --gender): F
+Number of reads: 2081160
+Standard deviation of the ratios per chromosome: 0.00932
+Median segment variance per bin (doi: 10.1093/nar/gky1263): 0.0008
+Copy number profile abnormality (CPA) score (doi: 10.1186/s13073-020-00735-4): 2.32398
diff --git a/tools/wisecondorx/wisecondor_npz_converter.xml b/tools/wisecondorx/wisecondor_npz_converter.xml
new file mode 100644
index 00000000..7f86b7e6
--- /dev/null
+++ b/tools/wisecondorx/wisecondor_npz_converter.xml
@@ -0,0 +1,57 @@
+
+
+ bam to npz
+
+
+ macro.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+@help@
+
+
+ 10.1093/nar/gky1263
+
+
diff --git a/tools/wisecondorx/wisecondor_predict.xml b/tools/wisecondorx/wisecondor_predict.xml
new file mode 100644
index 00000000..44fa5568
--- /dev/null
+++ b/tools/wisecondorx/wisecondor_predict.xml
@@ -0,0 +1,112 @@
+
+
+ CNVs
+
+
+ macro.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+@help@
+ mean + sd * 3 in the reference will be
+ masked. This parameter represents the number of masking cycles
+ and defines the stringency of the blacklist (default: x=5)
+ **Should be a multiple of the 5e3**.
+ Not exposed in this Galaxy wrapper.
+ --zscore Z-score cutoff to call segments as aberrations (default: x=5)
+ --alpha P-value cutoff for calling circular binary segmentation
+ breakpoints (default: x=1e-4).
+ Not exposed in this Galaxy wrapper.
+ --beta When beta is given, --zscore is ignored. Beta sets a ratio
+ cutoff for aberration calling. It's a number between 0 (liberal)
+ and 1 (conservative) and, when used, is optimally close to the
+ purity (e.g. fetal/tumor fraction)
+ Not exposed in this Galaxy wrapper.
+ --blacklist Blacklist for masking additional regions; requires headerless
+ .bed file. This is particularly useful when the reference set
+ is too small to recognize some obvious loci (such as centromeres).
+ Not exposed in this Galaxy wrapper.
+ --gender Force WisecondorX to analyze this case as male (M) or female (F).
+ Useful when e.g. dealing with a loss of chromosome Y, which
+ causes erroneous gender predictions (choices: x=F or x=M).
+ Not exposed in this Galaxy wrapper.
+ --bed Outputs tab-delimited .bed files.
+ --plot Outputs custom .png plots, directly interpretable.
+ --ylim [a,b] Force WisecondorX to use y-axis interval [a,b] during plotting, e.g. [-2,2].
+ Not exposed in this Galaxy wrapper.
+ --cairo Some operating systems require the cairo bitmap type to write plots.
+ Not exposed in this Galaxy wrapper.
+ --seed Random seed for segmentation algorithm (default:None).
+ Not exposed in this Galaxy wrapper.
+ ]]>
+
+ 10.1093/nar/gky1263
+
+
diff --git a/tools/wisecondorx/wisecondor_reference_builder.xml b/tools/wisecondorx/wisecondor_reference_builder.xml
new file mode 100644
index 00000000..e6e02b14
--- /dev/null
+++ b/tools/wisecondorx/wisecondor_reference_builder.xml
@@ -0,0 +1,66 @@
+
+
+ reference
+
+
+ macro.xml
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+@help@
+
+
+ 10.1093/nar/gky1263
+
+