Mercurial > repos > iuc > bwa_mem2

changeset 5:fea76fc17330 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2 commit 9b90dfa03f17a23ca1fb2f745ffdc03de6256560
author iuc
date Fri, 28 Mar 2025 08:29:39 +0000
parents d3e88507ee64
children d459a463cb73
files bwa-mem2.xml macros.xml
diffstat 2 files changed, 109 insertions(+), 53 deletions(-) [+]
line wrap: on
line diff
--- a/bwa-mem2.xml	Wed Mar 19 17:25:56 2025 +0000
+++ b/bwa-mem2.xml	Fri Mar 28 08:29:39 2025 +0000
@@ -4,8 +4,10 @@
         <import>read_group_macros.xml</import>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"/>
     <expand macro="xrefs"/>
+    <expand macro="requirements">
+        <requirement type="package" version="1.21">samtools</requirement>
+    </expand>
     <expand macro="stdio"/>
     <command><![CDATA[
 @pipefail@
@@ -282,80 +284,134 @@
 
     <tests>
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="bwa_mem2_index" class="Directory" value="test-cache"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
+                <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
         </test>
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
+                <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
         </test>
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="single"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="single"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="6" />
         </test>
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired"/>
+                <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/>
+                <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
         </test>
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <param name="rg_selector" value="set"/>
-            <param name="ID" value="rg1"/>
-            <param name="PL" value="CAPILLARY"/>
-            <param name="LB" value="AARDVARK-1" />
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
+                <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            </conditional>
+            <conditional name="rg">
+                <param name="rg_selector" value="set"/>
+                <conditional name="read_group_id_conditional">
+                    <param name="ID" value="rg1"/>
+                </conditional>
+                    <conditional name="read_group_lb_conditional">
+                    <param name="LB" value="AARDVARK-1" />
+                </conditional>
+                <param name="PL" value="CAPILLARY"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <output name="bam_output" ftype="bam" file="bwa-mem-test2.bam" lines_diff="6" />
         </test>
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
+                <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <param name="output_sort" value="unsorted"/>
             <output name="bam_output" ftype="qname_input_sorted.bam" file="bwa-mem-test3.bam" lines_diff="6" />
         </test>
         <test>
-            <param name="reference_source_selector" value="history" />
-            <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history" />
+                <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
+                <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <param name="output_sort" value="name"/>
             <output name="bam_output" ftype="qname_sorted.bam" file="bwa-mem-test4.bam" lines_diff="6" />
         </test>
         <test>
-            <param name="reference_source_selector" value="cached" />
-            <param name="ref_file" value="mtgenome"/>
-            <param name="fastq_input_selector" value="paired"/>
-            <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
-            <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
-            <param name="analysis_type_selector" value="illumina"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached" />
+                <param name="ref_file" value="mtgenome"/>
+            </conditional>
+            <conditional name="fastq_input">
+                <param name="fastq_input_selector" value="paired"/>
+                <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
+                <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
+            </conditional>
+            <conditional name="analysis_type">
+                <param name="analysis_type_selector" value="illumina"/>
+            </conditional>
             <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="6" />
         </test>
     </tests>
--- a/macros.xml	Wed Mar 19 17:25:56 2025 +0000
+++ b/macros.xml	Fri Mar 28 08:29:39 2025 +0000
@@ -2,7 +2,7 @@
     <import>read_group_macros.xml</import>
 
     <token name="@TOOL_VERSION@">2.2.1</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE_VERSION@">20.01</token>
 
     <xml name="xrefs">