diff updio.xml @ 2:264bc77bfed6 draft

planemo upload commit b4edb673bebdba310129b925d36206b7e546efd0

--- a/updio.xml	Tue Jan 17 09:55:11 2023 +0000
+++ b/updio.xml	Wed Jan 18 05:12:49 2023 +0000
@@ -1,18 +1,19 @@
-<tool id="updio" name="UPDio" version="1.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="updio" name="UPDio" version="1.1.0+galaxy1" python_template_version="3.5" profile="21.05">
     <requirements>
         <requirement type="package" version="1.1.0">updio</requirement>
         <container type="docker">quay.io/biowdl/updio:1.1.0</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-       ln -s $multisample_vcf input.vcf &&
-        updio --multisample_vcf input.vcf
+       ln -s $multisample_vcf input.vcf.gz &&
+        updio --multisample_vcf input.vcf.gz
         --childID $child_id
         --momID $mom_id
         --dadID $dad_id &&
-        mv output_dir/${child_id}.table ${updio_table}
+        mv output_dir/${child_id}.table ${updio_table} &&
+        mv output_dir/${child_id}.upd ${updio_verdict}
     ]]></command>
     <inputs>
-        <param name="multisample_vcf" type="data" format="vcf"
+        <param name="multisample_vcf" type="data" format="vcf_bgzip"
                label="multisample VCF file" />
         <param name="child_id" type="text"
                label="child sample ID in the VCF file" />
@@ -23,6 +24,7 @@
     </inputs>
     <outputs>
         <data format="tsv" name="updio_table" label="${tool.name} on ${on_string}: table"/>
+        <data format="tsv" name="updio_verdict" label="${tool.name} on ${on_string}: verdict"/>
     </outputs>
     <help><![CDATA[
         UPDio is designed to detect UPD events in probands from vcf trio data.