WisecondorX galaxy wrapper (#696)

* ~64 commits to develop this first version of WisecondorX Galaxy wrapper

* Downgrading to release_23.1 for the ci tests !

Author: drosofff

.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:

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

tools/wisecondorx/macro.xml

@@ -0,0 +1,54 @@
+<macros>
+    <token name="@VERSION@">1.2.9</token>
+    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy0</token>
+    <token name="@PROFILE@">23.0</token>
+    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">wisecondorx</requirement>
+        </requirements>
+    </xml>
+<token name="@help@"><![CDATA[
+**What it does**
+
+WisecondorX, which uses a within-sample normalization technique, detects Copy
+Number Variation from BAM input files.
+
+It is important that **no** read quality filtering is executed prior to running
+WisecondorX: this software requires low-quality reads to distinguish informative
+bins from non-informative ones.
+
+There are three main stages (converting, reference build and predicting) when
+using WisecondorX:
+
+**1. Convert .bam files** of aligned reads to .npz files (for both normal and
+tumor samples) using the Galaxy tool **WisecondorX convert bam to npz**
+
+**2. Buid a reference index** from .npz files from **normal** samples using the
+Galaxy tool **WisecondorX build reference**.
+
+.. class:: warningmark
+
+Automated gender prediction, required to consistently analyze sex chromosomes,
+is based on a Gaussian mixture model. If few samples (<20) are included during
+reference creation, or not both male and female samples (for NIPT, this means
+male and female feti) are represented, this process might not be accurate.
+Therefore, alternatively, one can manually tweak the --yfrac parameter.
+
+.. class:: warningmark
+
+It is of paramount importance that the reference set consists of exclusively
+negative (normal) control samples that originate from the same sequencer, mapper,
+reference genome, type of material, ... etc, as the test samples. As a rule of
+thumb, think of all laboratory and in silico steps: the more sources of bias that
+can be omitted, the better.
+
+Try to include at least 50 samples per reference. The more the better, yet, from
+500 on it is unlikely to observe additional improvement concerning normalization.
+
+**3. Predict Copy Number Variantions** from the reference index and tumor .npz cases
+of interest using the Galaxy tool **WisecondorX predict CNVs**
+
+]]></token>
+</macros>