# HG changeset patch
# User rhpvorderman
# Date 1636123393 0
# Node ID 72d68e2e1fd3cae7623d6603510da49795128d34
# Parent  281329c035eee99b8258e15bca44420fee15d057
"planemo upload commit a8565b413cbe0ef70bc22994ecdd48b400ba6185"

diff -r 281329c035ee -r 72d68e2e1fd3 conda_environment.yml
--- a/conda_environment.yml	Fri Nov 05 10:59:28 2021 +0000
+++ b/conda_environment.yml	Fri Nov 05 14:43:13 2021 +0000
@@ -17,7 +17,9 @@
   - r-seqinr=3.4_5
   - r-data.table=1.11.4
   - file=5.39
+  - bc=1.07.1
+  - findutils=4.6.0
   # Test dependencies below
-  - pytest
+  - pytest=6.2.5
   # Add planemo so tool can be uploaded
-  - planemo
+  - planemo=0.74.9
diff -r 281329c035ee -r 72d68e2e1fd3 shm_csr.xml
--- a/shm_csr.xml	Fri Nov 05 10:59:28 2021 +0000
+++ b/shm_csr.xml	Fri Nov 05 14:43:13 2021 +0000
@@ -1,5 +1,5 @@
-<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.2.2">
-	<description>Performs a summary/analysis of an IMGT HighV-QUEST (https://www.imgt.org/HighV-QUEST/) ZIP file for Somatic hypermutation and class switch recombination.</description>
+<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.3.1">
+	<description></description>
 	<requirements>
 		<requirement type="package" version="3.7.1">python</requirement>
 		<requirement type="package" version="0.4.4">changeo</requirement>
@@ -16,7 +16,9 @@
 		<requirement type="package" version="4.4.18">bash</requirement>
 		<requirement type="package" version="1.34">tar</requirement>
 		<requirement type="package" version="5.39">file</requirement>
-		</requirements>
+		<requirement type="package" version="4.6.0">findutils</requirement>
+		<requirement type="package" version="1.07.1">bc</requirement>
+	</requirements>
 	<command interpreter="bash">
 		#if str ( $filter_unique.filter_unique_select ) == "remove":
 			wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter $fast
diff -r 281329c035ee -r 72d68e2e1fd3 tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc
Binary file tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc has changed
diff -r 281329c035ee -r 72d68e2e1fd3 wrapper.sh
--- a/wrapper.sh	Fri Nov 05 10:59:28 2021 +0000
+++ b/wrapper.sh	Fri Nov 05 14:43:13 2021 +0000
@@ -895,12 +895,12 @@
 echo "---------------- remove_files----------------"
 echo "---------------- remove_files----------------<br />" >> $log
 
-rm -r -v results/baseline
-rm -r -v files
+rm -r -v -f results/baseline
+rm -r -v -f files
 filename='remove_files.txt'
 
 while read file; do
-    rm -v $file
+    rm -v -f $file
 done < "$filename"