Merge pull request #34 from LUMC/baselinechangeo

Make baseline and changeO separately runnable
LUMC · Jan 10, 2024 · 079b489 · 079b489
2 parents 91fd26f + 546042a
commit 079b489
Show file tree

Hide file tree

Showing 4 changed files with 29 additions and 26 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,7 @@
+version 1.10.0-dev
+------------------
++ Replace "fast" option with options to toggle baseline and Change-O indidually.
+
 version 1.9.1
 -----------------
 + Fix error in launch command.

diff --git a/shm_csr.xml b/shm_csr.xml
@@ -1,4 +1,4 @@
-<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.9.1" profile="16.04">
+<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.10.0-dev" profile="16.04">
 	<description></description>
 	<requirements>
 		<requirement type="package" version="3.7.1">python</requirement>
@@ -35,7 +35,7 @@
 			$filter_unique.filter_unique_clone_count
 			$class_filter_cond.class_filter
 			$empty_region_filter
-			$fast
+			$changeo $baseline
 		#else:
 			$__tool_directory__/wrapper.sh "$in_file"
 			custom
@@ -48,7 +48,7 @@
 			2
 			$class_filter_cond.class_filter
 			$empty_region_filter
-			$fast
+			$changeo $baseline
 		#end if
 	]]>
 	</command>
@@ -108,59 +108,55 @@
 			</param>
 		</conditional>
 		<conditional name="naive_output_cond">
-			<param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
-				<option value="yes">Yes</option>
-				<option value="no" selected="true">No</option>
-			</param>
-			<when value="yes"></when>
-			<when value="no"></when>
-		</conditional>
-		<param name="fast" type="select" label="Fast" help="Skips Change-O/Baseline" >
-			<option value="yes">Yes</option>
-			<option value="no" selected="true">No</option>
-		</param>
+			<param name="naive_output" type="boolean" label="Output new IMGT archives per class into your history?"
+				   checked="no" truevalue="yes" falsevalue="no"/>
+			</conditional>
+		<param name="changeo" type="boolean" label="Run Change-O"
+			   checked="yes" truevalue="yes" falsevalue="no"/>
+		<param name="baseline" type="boolean" label="Run Baseline"
+			   checked="yes" truevalue="yes" falsevalue="no"/>
 	</inputs>
 	<outputs>
 		<data format="html" name="out_file" label = "SHM &amp; CSR on ${in_file.name}"/>
 		<data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" >
-		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>naive_output_cond['naive_output'] is True</filter>
 		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" >
-		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>naive_output_cond['naive_output'] is True</filter>
 		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" >
-		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>naive_output_cond['naive_output'] is True</filter>
 		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" >
-		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>naive_output_cond['naive_output'] is True</filter>
 		    <filter>class_filter_cond['class_filter'] != "101_101"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}">
-			<filter>naive_output_cond['naive_output'] == "yes"</filter>
+			<filter>naive_output_cond['naive_output'] is True</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}">
-			<filter>naive_output_cond['naive_output'] == "yes"</filter>
+			<filter>naive_output_cond['naive_output'] is True</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
 			<filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
 		</data>
 		<data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" >
-		    <filter>naive_output_cond['naive_output'] == "yes"</filter>
+		    <filter>naive_output_cond['naive_output'] is True</filter>
 		    <filter>class_filter_cond['class_filter'] == "101_101"</filter>
 		</data>
 	</outputs>

diff --git a/tests/test_shm_csr.py b/tests/test_shm_csr.py
@@ -84,7 +84,8 @@ def shm_csr_result():
     # anyway and take most of the test time to execute. The environment
     # variable can be set to "no" on the CI so the code path is tested
     # at the time a PR is ready.
-    fast = os.environ.get("SHM_CSR_FAST", "yes")
+    run_changeo = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no"
+    run_baseline = "yes" if os.environ.get("SHM_CSR_FAST") == "no" else "no"
     cmd = [
         "bash",
         wrapper,
@@ -108,7 +109,8 @@ def shm_csr_result():
         filter_unique_count,
         class_filter,
         empty_region_filter,
-        fast
+        run_changeo,
+        run_baseline
     ]
     docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}",
                   "--rm",  # Remove container after running

diff --git a/wrapper.sh b/wrapper.sh
@@ -22,7 +22,8 @@ filter_unique=${17}
 filter_unique_count=${18}
 class_filter=${19}
 empty_region_filter=${20}
-fast=${21}
+run_changeo=${21}
+run_baseline=${22}
 BASENAME=$(basename "$title")
 # Cut off .txz or .tgz suffix and also replace spaces with underscores.
 NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}"
@@ -410,7 +411,7 @@ count_imgt_lines () {
   rm 1_Summary.txt
 }
 
-if [[ "$fast" == "no" ]] ; then
+if [[ "$run_baseline" == "yes" ]] ; then
 
 
 
@@ -524,7 +525,7 @@ cat $dir/shm_csr.htm >> $output
 
 echo "</div>" >> $output #CSR tab end
 
-if [[ "$fast" == "no" ]] ; then
+if [[ "$run_changeo" == "yes" ]] ; then
 
 	echo "---------------- change-o MakeDB ----------------"