# HG changeset patch
# User galaxy-australia
# Date 1731294314 0
# Node ID 7ff7680fa7130902562215e2cb60b87d60f7f775
# Parent  1957f881bdf40c2ba5b0c8a422d066d5a664d52a
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 42ce963fae778982b4aab4ef3b1e88480dea5053

diff -r 1957f881bdf4 -r 7ff7680fa713 dorado_trimming.xml
--- a/dorado_trimming.xml	Mon Nov 04 03:27:55 2024 +0000
+++ b/dorado_trimming.xml	Mon Nov 11 03:05:14 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="dorado_trimming" name="Dorado adapter and primer trimming" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1">
+<tool id="dorado_trimming" name="Dorado adapter and primer trimming" version="@VERSION@+galaxy1" python_template_version="3.5" profile="24.1">
     <description>for Oxford Nanopore (ONT) DNA reads</description>
     <macros>
         <import>macros.xml</import>
@@ -14,11 +14,10 @@
 dorado trim
 --verbose
 --threads "\${GALAXY_SLOTS}"
-#if $no_trim_primers
+#if $trim_primers.no_trim_primers == 'dont_trim'
     --no-trim-primers
-#end if
-#if $primer_sequences
-    --primer-sequences '$primer_sequences'
+#else if $trim_primers.primer_sequences
+    --primer-sequences '${trim_primers.primer_sequences}'
 #end if
 reads
 > trimmed.bam
@@ -33,8 +32,16 @@
         ]]></command>
     <inputs>
         <param name="reads" type="data" format="bam,fastqsanger,unsorted.bam" label="Existing, basecalled DNA dataset" help="Note: this tool does not support trimming adaptors from RNA reads. These need to be removed during basecalling."/>
-        <param argument="--no-trim-primers" type="boolean" label="Don't trim primers" help="This option can be used to prevent the trimming of primer sequences. In this case only adapter sequences will be trimmed."/>
-        <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. The record names of the sequences do not matter. Note that if you use this option the normal primer sequences built-in to the dorado software will not be searched for."/>
+        <conditional name="trim_primers">
+            <param argument="--no-trim-primers" type="select" label="Enable primer trimming" help="Selecting 'No' prevents the trimming of primer sequences. In this case only adapter sequences will be trimmed.">
+                <option value="trim" selected="true">Yes</option>
+                <option value="dont_trim">No</option>
+            </param>
+            <when value="trim">
+                <param argument="--primer-sequences" type="data" format="fasta" optional="true" label="Custom primer sequences" help="You can specify an alternative set of primer sequences to search for when trimming by adding a FASTA file containing the primer sequences you want to search for. The record names of the sequences do not matter. Note that if you use this option the normal primer sequences built-in to the dorado software will not be searched for."/>
+            </when>
+            <when value="dont_trim"/>
+        </conditional>
     </inputs>
     <outputs>
         <data format="unsorted.bam" name="out_bam" label="Reads from ${on_string} trimmed by the ${tool.name} tool" from_work_dir="trimmed.bam"/>
@@ -43,20 +50,44 @@
     <tests>
         <test expect_num_outputs="2">
             <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/>
-            <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test1.bam"/>
-            <output name="out_tsv" ftype="tsv" file="dorado_trimming_test1.tsv"/>
+            <output name="out_bam" ftype="unsorted.bam">
+                <assert_contents>
+                    <has_size size="60725" delta="6000"/>
+                </assert_contents>
+            </output>
+            <output name="out_tsv" ftype="tsv">
+                <assert_contents>
+                    <has_text text="002f231b-5d37-437f-a027-a2e8b872e73b"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="2">
             <param name="reads" value="FAL00375_473bf0ed_0.ten_reads.bam"/>
-            <param name="no_trim_primers" value="True"/>
-            <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test2.bam"/>
-            <output name="out_tsv" ftype="tsv" file="dorado_trimming_test2.tsv"/>
+            <param name="no_trim_primers" value="dont_trim"/>
+            <output name="out_bam" ftype="unsorted.bam">
+                <assert_contents>
+                    <has_size size="60628" delta="6000"/>
+                </assert_contents>
+            </output>
+            <output name="out_tsv" ftype="tsv">
+                <assert_contents>
+                    <has_text text="00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf"/>
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="2">
             <param name="reads" value="lsk109_single_read.fastqsanger.gz" ftype="fastqsanger.gz"/>
             <param name="primer_sequences" value="custom_primers.fasta.gz" ftype="fasta.gz"/>
-            <output name="out_bam" ftype="unsorted.bam" file="dorado_trimming_test3.bam"/>
-            <output name="out_tsv" ftype="tsv" file="dorado_trimming_test3.tsv"/>
+            <output name="out_bam" ftype="unsorted.bam">
+                <assert_contents>
+                    <has_size size="798" delta="100"/>
+                </assert_contents>
+            </output>
+            <output name="out_tsv" ftype="tsv">
+                <assert_contents>
+                    <has_text text="2f707b6e-0060-4f33-9c92-a1230d26cb21"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
@@ -75,8 +106,9 @@
 of the barcodes being removed, which could interfere with correct
 demultiplexing.
 
-The **Don't trim primers** option can be used to prevent the trimming of
-primer sequences. In this case only adapter sequences will be trimmed.
+The **Enable primer trimming** option can be set to 'No' to prevent the
+trimming of primer sequences. If you select 'No', only adapter sequences will
+be trimmed.
 
 The output of will always be unaligned records, regardless of whether
 the input is aligned/sorted or not.
diff -r 1957f881bdf4 -r 7ff7680fa713 test-data/dorado_trimming_test1.bam
Binary file test-data/dorado_trimming_test1.bam has changed
diff -r 1957f881bdf4 -r 7ff7680fa713 test-data/dorado_trimming_test1.tsv
--- a/test-data/dorado_trimming_test1.tsv	Mon Nov 04 03:27:55 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-filename	read_id	run_id	channel	mux	start_time	duration	template_start	template_duration	sequence_length_template	mean_qscore_template	barcode
-reads.pod5	005cf7ae-4d74-42dd-ab96-9befed842822	473bf0edfc2f8f756173de35db5da9b6f6db4959	473	2	258.872	29.436	259.165	29.1435	14587	5.17895	unclassified
-reads.pod5	0066800d-d191-4833-a495-cfe8b925aca0	473bf0edfc2f8f756173de35db5da9b6f6db4959	56	4	359.11	14.0378	359.11	14.0378	5111	9.1072	unclassified
-reads.pod5	00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf	473bf0edfc2f8f756173de35db5da9b6f6db4959	300	3	329.733	2.5165	329.766	2.484	1055	12.9149	unclassified
-reads.pod5	002f231b-5d37-437f-a027-a2e8b872e73b	473bf0edfc2f8f756173de35db5da9b6f6db4959	118	3	534.745	19.5847	534.745	19.5847	8387	9.88254	unclassified
-reads.pod5	000a9728-0a7c-4b64-9791-76bb30b63796	473bf0edfc2f8f756173de35db5da9b6f6db4959	105	4	331.319	3.27625	331.319	3.27625	1175	12.0328	unclassified
-reads.pod5	0067486b-9f92-4849-8456-671463e64412	473bf0edfc2f8f756173de35db5da9b6f6db4959	84	4	164.018	2.453	164.018	2.453	885	12.399	unclassified
-reads.pod5	009f5efd-de5d-4a7e-9d17-969c3996cbc8	473bf0edfc2f8f756173de35db5da9b6f6db4959	230	2	171.634	3.27475	171.634	3.27475	1232	13.6258	unclassified
-reads.pod5	00aeb4ba-e404-49d2-97c5-8fcf22547f81	473bf0edfc2f8f756173de35db5da9b6f6db4959	51	4	297.891	50.1888	297.984	50.0962	19142	8.45178	unclassified
-reads.pod5	0072b26f-f37c-4517-afa7-621543ac2187	473bf0edfc2f8f756173de35db5da9b6f6db4959	317	3	111.275	2.31875	111.275	2.31875	929	9.69614	unclassified
-reads.pod5	00ad521b-b916-404f-a31d-a657f9aa7756	473bf0edfc2f8f756173de35db5da9b6f6db4959	365	2	566.263	23.6745	566.263	23.6745	10934	12.074	unclassified
diff -r 1957f881bdf4 -r 7ff7680fa713 test-data/dorado_trimming_test2.bam
Binary file test-data/dorado_trimming_test2.bam has changed
diff -r 1957f881bdf4 -r 7ff7680fa713 test-data/dorado_trimming_test2.tsv
--- a/test-data/dorado_trimming_test2.tsv	Mon Nov 04 03:27:55 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-filename	read_id	run_id	channel	mux	start_time	duration	template_start	template_duration	sequence_length_template	mean_qscore_template	barcode
-reads.pod5	00777c4b-cbd6-4a79-8647-bbe5f5f3f3bf	473bf0edfc2f8f756173de35db5da9b6f6db4959	300	3	329.733	2.5165	329.766	2.484	1055	12.9149	unclassified
-reads.pod5	0072b26f-f37c-4517-afa7-621543ac2187	473bf0edfc2f8f756173de35db5da9b6f6db4959	317	3	111.275	2.31875	111.275	2.31875	929	9.69614	unclassified
-reads.pod5	0067486b-9f92-4849-8456-671463e64412	473bf0edfc2f8f756173de35db5da9b6f6db4959	84	4	164.018	2.453	164.018	2.453	885	12.399	unclassified
-reads.pod5	002f231b-5d37-437f-a027-a2e8b872e73b	473bf0edfc2f8f756173de35db5da9b6f6db4959	118	3	534.745	19.5847	534.745	19.5847	8387	9.88254	unclassified
-reads.pod5	0066800d-d191-4833-a495-cfe8b925aca0	473bf0edfc2f8f756173de35db5da9b6f6db4959	56	4	359.11	14.0378	359.11	14.0378	5111	9.1072	unclassified
-reads.pod5	009f5efd-de5d-4a7e-9d17-969c3996cbc8	473bf0edfc2f8f756173de35db5da9b6f6db4959	230	2	171.634	3.27475	171.634	3.27475	1232	13.6258	unclassified
-reads.pod5	005cf7ae-4d74-42dd-ab96-9befed842822	473bf0edfc2f8f756173de35db5da9b6f6db4959	473	2	258.872	29.436	259.165	29.1435	14587	5.17895	unclassified
-reads.pod5	000a9728-0a7c-4b64-9791-76bb30b63796	473bf0edfc2f8f756173de35db5da9b6f6db4959	105	4	331.319	3.27625	331.319	3.27625	1175	12.0328	unclassified
-reads.pod5	00ad521b-b916-404f-a31d-a657f9aa7756	473bf0edfc2f8f756173de35db5da9b6f6db4959	365	2	566.263	23.6745	566.263	23.6745	10934	12.074	unclassified
-reads.pod5	00aeb4ba-e404-49d2-97c5-8fcf22547f81	473bf0edfc2f8f756173de35db5da9b6f6db4959	51	4	297.891	50.1888	297.984	50.0962	19142	8.45178	unclassified
diff -r 1957f881bdf4 -r 7ff7680fa713 test-data/dorado_trimming_test3.bam
Binary file test-data/dorado_trimming_test3.bam has changed
diff -r 1957f881bdf4 -r 7ff7680fa713 test-data/dorado_trimming_test3.tsv
--- a/test-data/dorado_trimming_test3.tsv	Mon Nov 04 03:27:55 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-filename	read_id	run_id	channel	mux	start_time	duration	template_start	template_duration	sequence_length_template	mean_qscore_template	barcode
-	2f707b6e-0060-4f33-9c92-a1230d26cb21	unknown	0	0	0	0	0	0	421	0	unclassified