diff artic_minion.xml @ 3:94020e19b46c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic commit 54e51c32ac2c1fdc5391ee44f749cf6617db5acb"

--- a/artic_minion.xml	Wed Jun 10 18:36:36 2020 -0400
+++ b/artic_minion.xml	Tue Sep 29 20:20:01 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy0">
+<tool id="artic_minion" name="ARTIC minion" version="1.1.3+galaxy1">
     <description>Build consensus sequence and call variants from amplicon-based nanopore sequence data</description>
     <requirements>
         <requirement type="package" version="1.1.3">artic</requirement>
@@ -19,17 +19,22 @@
         #end if
         artic minion
             --threads \${GALAXY_SLOTS:-1}
-            --normalise '${normalise}'
+        #if $normalise > 0:
+            --normalise ${normalise}
+        #end if
             --read-file '${read_file}'
             --scheme-directory 'scheme'
             --medaka
             $bwa
             'name/version'
             '${read_file.element_identifier}'
+        && bgzip -f '${read_file.element_identifier}.fail.vcf'
     ]]></command>
     <inputs>
         <param argument="--read-file" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Input Read File"/>
-        <param argument="--normalise" type="integer" min="1" value="200" max="2000" label="Coverage normalisation depth"/>
+        <param argument="--normalise" type="integer" min="0" value="0"
+        label="Coverage normalisation depth"
+        help="Sample at most this number of reads per amplicon and strand. default=0 (use all reads)" />
         <param argument="--bwa" type="boolean" truevalue="--bwa" falsevalue="" label="Use bwa aligner"/>
         <conditional name="primer_scheme_source">
             <param name="primer_scheme_source_selector" type="select" label="Select a primer scheme from your history or use one from a tool data table?"
@@ -68,14 +73,13 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="alignment_trimmed" format="bam" from_work_dir="*.trimmed.bam" label="${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 ${on_string}: variants merged" />
-        <data name="variants_pass_vcf" format="vcf_bgzip" from_work_dir="*.pass.vcf.gz" label="${tool.name} on ${on_string}: variants pass" />
-        <data name="variants_fail_vcf" format="vcf" from_work_dir="*.fail.vcf" label="${tool.name} on ${on_string}: variants fail" />
+        <data name="alignment_trimmed" format="bam" from_work_dir="*.primertrimmed.rg.sorted.bam" label="${tool.name} on ${on_string}: trimmed alignment" />
+        <data name="alignment_report" format="tabular" from_work_dir="*.alignreport.txt" label="${tool.name} on ${on_string}: alignment report" />
+        <data name="variants_merged_vcf" format="vcf_bgzip" from_work_dir="*.merged.vcf.gz" label="${tool.name} on ${on_string}: medaka variant calls" />
+        <data name="variants_fail_vcf" format="vcf_bgzip" from_work_dir="*.fail.vcf.gz" label="${tool.name} on ${on_string}: variants fail" />
+        <data name="variants_pass_vcf" format="vcf" from_work_dir="*.pass.vcf" label="${tool.name} on ${on_string}: variants pass" />
         <data name="consensus_fasta" format="fasta" from_work_dir="*.consensus.fasta" label="${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 ${on_string}: coverage mask" />
+        <data name="coverage_mask" format="tabular" from_work_dir="*.coverage_mask.txt" label="${tool.name} on ${on_string}: consensus coverage mask" />
         <data name="analysis_log" format="txt" from_work_dir="*.minion.log.txt" label="${tool.name} on ${on_string}: analysis log" />
     </outputs>
     <tests>