# HG changeset patch
# User rhpvorderman
# Date 1639485947 0
# Node ID 7ae6b6b5d890f3797d35951ab06e7af2c154239b
# Parent  2a7dc86d8f85bbc620327553e934f749a33eb0f8
"planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"

diff -r 2a7dc86d8f85 -r 7ae6b6b5d890 complete_immunerepertoire.xml
--- a/complete_immunerepertoire.xml	Fri Nov 19 10:09:54 2021 +0000
+++ b/complete_immunerepertoire.xml	Tue Dec 14 12:45:47 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.0.2">
+<tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.1.0.alpha1">
 	<requirements>
         <requirement type="package" version="2.3">r-gridextra</requirement>
         <requirement type="package" version="3.0.0">r-ggplot2</requirement>
@@ -10,7 +10,13 @@
         <requirement type="package" version="1.3.1">r-stringr</requirement>
         <requirement type="package" version="0.69.6">circos</requirement>
         <requirement type="package" version="0.23">circos-tools</requirement>
-    </requirements>
+	  	<requirement type="package" version="1.34">tar</requirement>
+		<requirement type="package" version="6.0">unzip</requirement>
+		<requirement type="package" version="0.4">unrar</requirement>
+		<requirement type="package" version="16.02">p7zip</requirement>
+		<requirement type="package" version="4.6.0">findutils</requirement>
+   		<container type="docker">quay.io/rhpvorderman/mulled-v2-62aaeb9dad7d9973e676594c3aa69e605c73cd0c:80328e762d48b0d7b11c4fa41a5c09ca43d49db9-0</container>
+	</requirements>
 	<description> </description>
 	<command interpreter="bash">
 complete.sh "
@@ -32,7 +38,12 @@
 			<repeat name="samples" title="Replicate" min="1" default="1">
 					<param name="sample" type="data" label="Replicate to Process" />
 			</repeat>
-			<param name="id" type="text" label="ID" />
+			<param name="id" type="text" label="ID">
+				<!-- This replace whitespace with _ -->
+				<sanitizer invalid_char="_" sanitize="true">
+					<valid initial="default"/>
+				</sanitizer>
+			</param>
 		</repeat>
 		<param name="clonaltype" type="select" label="Clonal Type Definition">
 			<option value="none">Don't remove duplicates based on clonaltype</option>
diff -r 2a7dc86d8f85 -r 7ae6b6b5d890 conda_environment.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/conda_environment.yml	Tue Dec 14 12:45:47 2021 +0000
@@ -0,0 +1,25 @@
+name: argalaxy-immunerepertoire
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - imperial-college-research-computing
+dependencies:
+  - r-gridextra=2.3
+  - r-ggplot2=3.0.0
+  - r-plyr=1.8.4
+  - r-reshape2=1.4.3
+  - r-data.table=1.11.4
+  - r-lymphclon=1.3.0
+  - r-stringi=1.2.4
+  - r-stringr=1.3.1
+  - circos=0.69.6
+  - circos-tools=0.23
+  - bash=4.4.18
+  - file=5.39
+  - font-ttf-ubuntu=0.83
+  - tar=1.34
+  - unzip=6.0
+  - unrar=0.4
+  - p7zip=16.02
+  - findutils=4.6.0
\ No newline at end of file
diff -r 2a7dc86d8f85 -r 7ae6b6b5d890 mulled_container_build.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mulled_container_build.tsv	Tue Dec 14 12:45:47 2021 +0000
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+r-gridextra=2.3,r-ggplot2=3.0.0,r-plyr=1.8.4,r-reshape2=1.4.3,r-data.table=1.11.4,r-lymphclon=1.3.0,r-stringi=1.2.4,r-stringr=1.3.1,circos=0.69.6,circos-tools=0.23,bash=4.4.18,file=5.39,font-ttf-ubuntu=0.83,tar=1.34,unzip=6.0,unrar=0.4,p7zip=16.02,findutils=4.6.0	bgruening/busybox-bash:0.1	0
diff -r 2a7dc86d8f85 -r 7ae6b6b5d890 tests/__pycache__/test_imgt.cpython-39-pytest-6.2.5.pyc
Binary file tests/__pycache__/test_imgt.cpython-39-pytest-6.2.5.pyc has changed
diff -r 2a7dc86d8f85 -r 7ae6b6b5d890 tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz
Binary file tests/data/CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz has changed
diff -r 2a7dc86d8f85 -r 7ae6b6b5d890 tests/test_imgt.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tests/test_imgt.py	Tue Dec 14 12:45:47 2021 +0000
@@ -0,0 +1,89 @@
+# Copyright (c) 2021 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import os
+import shutil
+import subprocess
+import tempfile
+from pathlib import Path
+from xml.etree import ElementTree
+from xml.etree.ElementTree import Element
+
+import pytest
+
+GIT_ROOT = Path(__file__).parent.parent.absolute()
+TEST_DIR = Path(__file__).parent
+TEST_DATA_DIR = TEST_DIR / "data"
+VALIDATION_DATA_DIR = TEST_DIR / "validation_data"
+CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
+
+
+def get_container():
+    tool = ElementTree.parse(GIT_ROOT / "complete_immunerepertoire.xml").getroot()
+    requirements: Element = tool.find("requirements")
+    container = requirements.find("container")
+    return container.text
+
+
+@pytest.fixture(scope="module")
+def imgt_result():
+    temp_dir = Path(tempfile.mkdtemp())
+    tool_dir = temp_dir / "imgt"
+    shutil.copytree(GIT_ROOT, tool_dir)
+    working_dir = temp_dir / "working"
+    working_dir.mkdir(parents=True)
+    output_dir = temp_dir / "outputs"
+    output_dir.mkdir(parents=True)
+    wrapper = str(tool_dir / "complete.sh")
+    sample = CONTROL_NWK377_PB_IGHC_MID1_40nt_2
+    input = f"\"ID1\" {sample} {sample} \"ID2\" {sample}"
+    out_files_path = output_dir / "results"
+    out_files_path.mkdir(parents=True)
+    out_file = out_files_path / "result.html"
+    clonaltype = "none"
+    gene_selection = dict(species="Homo sapiens functional",
+                          locus="TRA")
+    filterproductive = "yes"
+    clonality_method = "none"
+    cmd = [
+        "bash",
+        wrapper,
+        input,
+        str(out_file),
+        str(out_files_path),
+        clonaltype,
+        gene_selection["species"],
+        gene_selection["locus"],
+        filterproductive,
+        clonality_method
+    ]
+    docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
+                  "-v", f"{sample}:{sample}",
+                  "-w", str(working_dir),
+                  get_container()] + cmd
+    with open(temp_dir / "stderr", "wt") as stderr_file:
+        with open(temp_dir / "stdout", "wt") as stdout_file:
+            subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file,
+                           stderr=stderr_file, check=True)
+    yield Path(out_files_path)
+
+
+def test_check_output(imgt_result):
+    assert imgt_result.exists()