Mercurial > repos > iuc > clair3

changeset 4:c9218b9dc7f0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510
author iuc
date Wed, 19 Feb 2025 16:19:04 +0000
parents 3843a30053ee
children
files clair3.xml test-data/clair3_models.loc test-data/full_alignment_1.vcf.gz test-data/merge_output_1.vcf.gz test-data/output_cram_test.vcf.gz test-data/phased_vcf_1.vcf.gz test-data/pileup_1.vcf.gz tool-data/model.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 10 files changed, 54 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/clair3.xml	Mon Sep 09 09:10:43 2024 +0000
+++ b/clair3.xml	Wed Feb 19 16:19:04 2025 +0000
@@ -1,7 +1,7 @@
 <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
     <description>germline small variant caller for long-reads</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.0.8</token>
+        <token name="@TOOL_VERSION@">1.0.10</token>
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <xrefs>
@@ -20,7 +20,11 @@
         samtools faidx reference.fasta &&
 
         #if $model_source.source == "datatable"
-            #set model_path = $model_source.model.fields.path 
+            #set model_path = $model_source.model.fields.path
+            #if $model_source.model.fields.source == "rerio" and $ont_license_agree != "true"
+                echo "You must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement to use Rerio models." >&2 &&
+                exit 2 ;
+            #end if   
         #end if
         #set $extension = $bam_input.ext
         ln -s '${$bam_input}' input_reads.$extension &&
@@ -93,6 +97,11 @@
                 </param>
             </when>
         </conditional>
+        <param name="ont_license_agree"
+            label="I agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement"
+            type="boolean" checked="false"
+            help="To use Rerio models (e.g. for ONT R10 chemistry) you must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement, which can be found in the nanoporetech/rerio Github repository."
+        />
         <conditional name="model_source">
             <param name="source" type="select" label="Clair3 model" help="Select if you want to use a built-in model shipping with the tool or a model cached on this Galaxy server.">
                 <option value="built-in">Built-in</option>
@@ -271,12 +280,44 @@
             </conditional>
             <output name="merge_output" decompress="true" file="output_cram_test.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
         </test>
+        <!-- test5 -->
+        <!-- Test the working of the ont_license_agree checkbox -->
+        <test expect_failure="true" expect_exit_code="2">
+            <conditional name="model_source">
+                <param name="source" value="datatable" />
+                <param name="model" value="r1041_e82_400bps_sup_v500" />
+            </conditional>
+            <param name="ont_license_agree" value="false" />
+            <!-- the rest of the parameters are included for completeness, as this test
+             should fail to run because of the license terms conflict -->
+            <param name="bam_input" value="test1.bam" />
+            <conditional name="ref_source">
+                <param name="source" value="history" />
+                <param name="ref_fasta" value="test1.fasta" />
+            </conditional>
+            <conditional name="bed_or_vcf">
+                <param name="bed_or_vcf_selector" value="vcf"/>
+                <param name="vcf_fn" value="test1.vcf.gz" />
+            </conditional>
+            <section name="adv">
+                <param name="no_phasing_for_fa" value="true"/>
+                <param name="print_ref_calls" value="true"/>
+                <param name="ploidity_model" value=""/>
+            </section>
+            <assert_stderr>
+                <has_line line="You must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement to use Rerio models." />
+            </assert_stderr>
+        </test>
     </tests>
     <help><![CDATA[
       Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:
       pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.
       Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.
       
+      The tool can use models from the Oxford Nanopore Technologies Rerio_ repository, which are covered by a license that restricts their use to
+      non-commercial use. If you select one of these models, you must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License,
+      which can be found in the Rerio repository in the file LICENSE.txt.
+
       https://github.com/HKU-BAL/Clair3
 
       LICENSE:
@@ -307,6 +348,8 @@
         ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
         (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
         SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+    .. _Rerio: https://github.com/nanoporetech/rerio
     ]]></help>
     <citations>
         <citation type="doi">10.1101/2021.12.29.474431</citation>
--- a/test-data/clair3_models.loc	Mon Sep 09 09:10:43 2024 +0000
+++ b/test-data/clair3_models.loc	Wed Feb 19 16:19:04 2025 +0000
@@ -4,7 +4,8 @@
 #for each build). This file has the format (white space characters are
 #TAB characters):
 #
-#<unique_build_id>  <display_name>   <platform> <file_path>
+#<unique_build_id>  <display_name>   <platform> <file_path>	<source>
 #
 #So, all_model.loc could look something like this:
-test_model	"the_model_name"	ont	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422
+test_model	"the_model_name"	ont	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
+r1041_e82_400bps_sup_v500	r1041_e82_400bps_sup_v500	ont	/no/such/model	rerio
Binary file test-data/full_alignment_1.vcf.gz has changed
Binary file test-data/merge_output_1.vcf.gz has changed
Binary file test-data/output_cram_test.vcf.gz has changed
Binary file test-data/phased_vcf_1.vcf.gz has changed
Binary file test-data/pileup_1.vcf.gz has changed
--- a/tool-data/model.loc.sample	Mon Sep 09 09:10:43 2024 +0000
+++ b/tool-data/model.loc.sample	Wed Feb 19 16:19:04 2025 +0000
@@ -4,7 +4,8 @@
 #for each build). This file has the format (white space characters are
 #TAB characters):
 #
-#<unique_build_id>  <display_name>   <platform> <file_path>
+#<unique_build_id>  <display_name>   <platform> <file_path>	<source>
 #
 #So, all_model.loc could look something like this:
-#test_model	"the_model_name"	r941_prom_hac_g360+g422	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422
+#test_model	r941_prom_hac_g360+g422		ont	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	clair3
+#r1041_e82_400bps_sup_v500	r1041_e82_400bps_sup_v500	ont	$(dirname $(which run_clair3.sh))/models/r941_prom_hac_g360+g422	rerio
--- a/tool_data_table_conf.xml.sample	Mon Sep 09 09:10:43 2024 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Feb 19 16:19:04 2025 +0000
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
 <tables>
-    <!-- Locations of indexes in the Bowtie mapper format -->
+    <!-- Locations of clair3 model folders -->
     <table name="model" comment_char="#">
-        <columns>value, name, platform, path</columns>
+        <columns>value, name, platform, path, source</columns>
         <file path="tool-data/model.loc" />
     </table>
     <table name="all_fasta" comment_char="#">
--- a/tool_data_table_conf.xml.test	Mon Sep 09 09:10:43 2024 +0000
+++ b/tool_data_table_conf.xml.test	Wed Feb 19 16:19:04 2025 +0000
@@ -2,7 +2,7 @@
 <tables>
     <!-- Locations of model folders -->
     <table name="clair3_models" comment_char="#">
-        <columns>value, name, platform, path</columns>
+        <columns>value, name, platform, path, source</columns>
         <file path="${__HERE__}/test-data/clair3_models.loc" />
     </table>
     <!-- Locations of reference genome files in fasta format -->