--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gen_bcv.xml	Tue Aug 05 09:20:46 2025 +0000
@@ -0,0 +1,45 @@
+<tool id="pimento_gen_bcv" name="PIMENTO Generate base-conservation vector(s)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENSE@">
+    <description>for primer fastq files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="creators"/>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+        pimento gen_bcv -i '$input_fastq' -st $strand -o sample
+    ]]></command>
+    <inputs>
+        <param name="input_fastq" type="data" label="Input reads to generate the BCV for" format="fastqsanger.gz"/>
+        <param name="strand" type="select" label="The strand(s) to generate a BCV for">
+            <option value="F">Forward</option>
+            <option value="R">Reverse</option>
+            <option value="FR">Forward and reverse</option>
+        </param>
+    </inputs>    
+    <outputs>
+        <data name="output" label="${tool.name} on ${on_string}: Base-conservation vector(s)" format="tsv" from_work_dir="sample_bcv.tsv"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_fastq" value="test.fastq.gz"/>
+            <param name="strand" value="FR"/>
+            <output name="output">
+                <assert_contents>
+                    <has_text text="F"/>
+                    <has_text text="0.9583999999999999"/>
+                    <has_text text="R"/>
+                    <has_text text="0.7263999999999999"/>
+                    <has_n_columns n="24"/>
+                    <has_n_lines n="3"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[ 
+        Generates base-conservation vector(s) for input fastq files. To be used by
+        the primer cutoff inference strategy, this function computes the base-
+        conservation vector for input reads. Users can choose to perform this
+        computation for either forward or reverse strands of the reads, or both.
+    ]]></help>
+    <expand macro="citations" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Aug 05 09:20:46 2025 +0000
@@ -0,0 +1,20 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.0.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@LICENSE@">Apache-2.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">mi-pimento</requirement>
+        </requirements>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082" identifier="https://orcid.org/0009-0000-2501-8053"/>
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/2025.07.04.663168</citation>
+        </citations>
+    </xml>
+</macros>

Binary file test-data/test.fastq.gz has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bcv.tsv	Tue Aug 05 09:20:46 2025 +0000
@@ -0,0 +1,3 @@
+	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24
+F	0.952	0.9583999999999999	0.96	0.8464	0.8552	0.8343999999999999	0.8112	0.7272	0.828	0.8071999999999999	0.8039999999999999	0.8055999999999999	0.8736	0.8343999999999999	0.8432000000000001	0.8231999999999999	0.8200000000000001	0.836	0.8720000000000001	0.876	0.8168	0.8352	0.8216000000000001
+R	0.9544	0.8472	0.7263999999999999	0.7295999999999999	0.7287999999999999	0.7248	0.8256	0.9408	0.9336	0.9352	0.9328000000000001	0.9359999999999999	0.9368000000000001	0.9384	0.9399999999999998	0.9416	0.8888	0.8880000000000001	0.8928	0.8943999999999999	0.8768	0.9256	0.9199999999999999

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_cutoffs.tsv	Tue Aug 05 09:20:46 2025 +0000
@@ -0,0 +1,3 @@
+strand	inf_point
+F	14
+R	17