From 09a61459616af34ed5c08400b9a18af5bf30dfec Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Thu, 18 Jul 2024 09:24:55 +0200
Subject: [PATCH] simplify argument names

---
 .../umi_tools_extract/config.vsh.yaml          |  8 +++-----
 src/umi_tools/umi_tools_extract/script.sh      |  4 ++--
 src/umi_tools/umi_tools_extract/test.sh        | 18 +++++++++---------
 3 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/src/umi_tools/umi_tools_extract/config.vsh.yaml b/src/umi_tools/umi_tools_extract/config.vsh.yaml
index 2972820c..5eb8ac16 100644
--- a/src/umi_tools/umi_tools_extract/config.vsh.yaml
+++ b/src/umi_tools/umi_tools_extract/config.vsh.yaml
@@ -59,8 +59,7 @@ argument_groups:
 
   - name: Extract Options
     arguments:
-    - name: --umitools_extract_method
-      alternatives: --extract_method
+    - name: --extract_method
       type: string
       choices: [string, regex]
       description: |
@@ -116,14 +115,13 @@ argument_groups:
         Ignore "/1" and "/2" read name suffixes. Note that this options is required if the suffixes are not whitespace
         separated from the rest of the read name.
         arguments:
-    - name: --umitools_umi_separator
-      alternatives: --umi_separator
+    - name: --umi_separator
       type: string
       description: |
         The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with
         UMI-tools and used other software. Default: `_`
       example: "_"
-    - name: --umitools_grouping_method
+    - name: --grouping_method
       type: string
       choices: [unique, percentile, cluster, adjacency, directional]
       description: |
diff --git a/src/umi_tools/umi_tools_extract/script.sh b/src/umi_tools/umi_tools_extract/script.sh
index dfa95bca..32958c16 100644
--- a/src/umi_tools/umi_tools_extract/script.sh
+++ b/src/umi_tools/umi_tools_extract/script.sh
@@ -43,10 +43,10 @@ umi_tools extract \
     ${par_read2_in:+ --read2-in "$par_read2_in"} \
     -S "$par_read1_out" \
     ${par_read2_out:+--read2-out "$par_read2_out"} \
-    ${par_umitools_extract_method:+--extract-method "$par_umitools_extract_method"} \
+    ${par_extract_method:+--extract-method "$par_extract_method"} \
     --bc-pattern "$par_bc_pattern" \
     ${par_bc_pattern2:+ --bc-pattern2 "$par_bc_pattern2"} \
-    ${par_umitools_umi_separator:+--umi-separator "$par_umitools_umi_separator"} \
+    ${par_umi_separator:+--umi-separator "$par_umi_separator"} \
     ${par_output_stats:+--output-stats "$par_output_stats"} \
     ${par_error_correct_cell:+--error-correct-cell} \
     ${par_whitelist:+--whitelist "$par_whitelist"} \
diff --git a/src/umi_tools/umi_tools_extract/test.sh b/src/umi_tools/umi_tools_extract/test.sh
index e9c13e27..ed8d4741 100644
--- a/src/umi_tools/umi_tools_extract/test.sh
+++ b/src/umi_tools/umi_tools_extract/test.sh
@@ -13,9 +13,9 @@ echo ">>> Test 1: Testing for paired-end reads"
     --read2_in "$test_dir/scrb_seq_fastq.2_30" \
     --bc_pattern "CCCCCCNNNNNNNNNN"\
     --bc_pattern2 "CCCCCCNNNNNNNNNN" \
-    --umitools_extract_method string \
-    --umitools_umi_separator '_' \
-    --umitools_grouping_method directional \
+    --extract_method string \
+    --umi_separator '_' \
+    --grouping_method directional \
     --umi_discard_read 0 \
     --read1_out scrb_seq_fastq.1_30.extract \
     --read2_out scrb_seq_fastq.2_30.extract \
@@ -44,9 +44,9 @@ echo ">>> Test 2: Testing for paired-end reads with umi_discard_reads option"
     --read2_in "$test_dir/scrb_seq_fastq.2_30" \
     --bc_pattern CCCCCCNNNNNNNNNN \
     --bc_pattern2 CCCCCCNNNNNNNNNN \
-    --umitools_extract_method string \
-    --umitools_umi_separator '_' \
-    --umitools_grouping_method directional \
+    --extract_method string \
+    --umi_separator '_' \
+    --grouping_method directional \
     --umi_discard_read 2 \
     --read1_out scrb_seq_fastq.1_30.extract \
     --random_seed 1
@@ -68,9 +68,9 @@ echo ">>> Test 3: Testing for single-end reads"
 "$meta_executable" \
     --input "$test_dir/slim_30.fastq" \
     --bc_pattern "^(?P<umi_1>.{3}).{4}(?P<umi_2>.{2})" \
-    --umitools_extract_method regex \
-    --umitools_umi_separator '_' \
-    --umitools_grouping_method directional \
+    --extract_method regex \
+    --umi_separator '_' \
+    --grouping_method directional \
     --read1_out slim_30.extract \
     --random_seed 1