diff artic_minion.xml @ 1:20165d3a8fb1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 125ea4d98050db32bae4f722ef153305e8d48a94"

--- a/artic_minion.xml	Thu Apr 30 04:05:09 2020 -0400
+++ b/artic_minion.xml	Wed Jun 10 14:30:19 2020 -0400
@@ -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' &&
@@ -38,14 +38,14 @@
                 <option value="history">From history</option>
             </param>
             <when value="tool_data_table">
-                <param name="primer_scheme_bedfile" type="select" format="bed" label="Primer Scheme">
+                <param name="primer_scheme_bedfile" type="select" format="tabular" label="Primer Scheme">
 	            <options from_data_table="primer_scheme_bedfiles">
 	                <validator type="no_options" message="No primer scheme .bed files are available" />
                     </options>
 	        </param>
             </when>
             <when value="history">
-                <param name="primer_scheme_bedfile" type="data" format="bed" label="Primer Scheme" />
+                <param name="primer_scheme_bedfile" type="data" format="tabular" label="Primer Scheme" />
             </when>
         </conditional>
         <conditional name="reference_source">
@@ -70,33 +70,38 @@
     <outputs>
         <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 ${on_string}: variants vcf" />
+        <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${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.V1.bed" />
-            <output name="consensus_fasta" file="SRR11410539_seqtk_sample_250_1.fastq.consensus.fasta" />
+            <param name="primer_scheme_bedfile" value="nCoV-2019.scheme.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[