# HG changeset patch
# User dfornika
# Date 1591651839 0
# Node ID 39c2f17a4ad44f65430fb5f5df39630bf3110005
# Parent  08558c991bf8ae4a83a6b6712f260d697211fb17
Uploaded

diff -r 08558c991bf8 -r 39c2f17a4ad4 artic_minion.xml
--- a/artic_minion.xml	Wed Apr 29 17:02:01 2020 +0000
+++ b/artic_minion.xml	Mon Jun 08 21:30:39 2020 +0000
@@ -1,7 +1,7 @@
-<tool id="artic_minion" name="ARTIC minion" version="1.1.0_rc2+galaxy0">
-    <description></description>
+<tool id="artic_minion" name="ARTIC minion" version="1.1.2+galaxy0">
+    <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
     <requirements>
-        <requirement type="package" version="1.1.0_rc2">artic</requirement>
+        <requirement type="package" version="1.1.2">artic</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p 'scheme/name/version' &&
@@ -28,7 +28,7 @@
             '${read_file.element_identifier}'
     ]]></command>
     <inputs>
-        <param name="read_file" argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
+        <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
         <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/>
         <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
         <conditional name="primer_scheme_source">
@@ -68,35 +68,40 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="" />
-        <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="" />
-        <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="" />
-        <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="" />
+        <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
+        <data name="variants_tabular" format="tabular" from_work_dir="*.variants.tab" label="${tool.name} on ${on_string}: variants table" />
+        <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: variants merged" />
+        <data name="variants_pass_vcf" format="vcf_bgzip" from_work_dir="*.pass.vcf.gz" label="${tool.name} on ${on_string}: variants pass" />
+        <data name="variants_fail_vcf" format="vcf" from_work_dir="*.fail.vcf" label="${tool.name} on ${on_string}: variants fail" />
+        <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${tool.name} on ${on_string}: consensus sequence" />
+        <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
+        <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: coverage mask" />
+        <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" />
     </outputs>
     <tests>
         <test>
             <param name="reference_source_selector" value="history" />
-            <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" />
+            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
             <param name="reference" value="nCoV-2019.reference.fasta" />
             <param name="primer_scheme_source_selector" value="tool_data_table" />
             <param name="primer_scheme_bedfile" value="test_entry" />
-            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
+            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
         </test>
         <test>
             <param name="reference_source_selector" value="history" />
-            <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" />
+            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
             <param name="reference" value="nCoV-2019.reference.fasta" />
             <param name="primer_scheme_source_selector" value="history" />
-            <param name="primer_scheme_bedfile" value="nCoV-2019.scheme.V3.bed" />
-            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
+            <param name="primer_scheme_bedfile" value="nCoV-2019.V1.bed" />
+            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
         </test>
         <test>
             <param name="reference_source_selector" value="tool_data_table" />
-            <param name="read_file" value="SRR11410539_seqtk_sample_250_1.fastq" />
+            <param name="read_file" value="SRR11410539_seqtk_sample_500_1.fastq" />
             <param name="reference" value="test_entry" />
             <param name="primer_scheme_source_selector" value="tool_data_table" />
             <param name="primer_scheme_bedfile" value="test_entry" />
-            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
+            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_500_1.fastq.consensus.fasta" />
         </test>
     </tests>
     <help><![CDATA[