diff updio.xml @ 0:0bc9750fc1db draft default tip

planemo upload commit 1b7d98a104f966bbc5edbbee79160b8994b57081

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/updio.xml	Wed Dec 13 15:41:00 2023 +0000
@@ -0,0 +1,56 @@
+<tool id="updio" name="UPDio" version="1.1.0+galaxy3" python_template_version="3.5" profile="21.05">
+    <requirements>
+        <requirement type="package" version="1.1.0">updio</requirement>
+        <container type="docker">quay.io/biocontainers/updio:1.1.0--hdfd78af_0</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+       #if str($input_type.input_type_selector) == "file"
+         #from pathlib import Path
+         #set $child_id = Path(str($input_type.child_id_file)).read_text().strip()
+         #set $mother_id = Path(str($input_type.mother_id_file)).read_text().strip()
+         #set $father_id = Path(str($input_type.father_id_file)).read_text().strip()
+       #end if
+       ln -s $multisample_vcf input.vcf.gz &&
+        updio --multisample_vcf input.vcf.gz
+        --childID $child_id
+        --momID $mother_id
+        --dadID $father_id &&
+        mv output_dir/${child_id}.table ${updio_table} &&
+        mv output_dir/${child_id}.upd ${updio_verdict}
+    ]]></command>
+    <inputs>
+        <param name="multisample_vcf" type="data" format="vcf_bgzip"
+           label="multisample VCF file" />
+        <param name="output_label" type="text"
+           label="Analysis name, to distinguish the output." />
+        <conditional name="input_type">
+            <param name="input_type_selector" type="select" label="Sample IDs submitted by:">
+                <option value="text" selected="true">Text</option>
+                <option value="file">Files (for easier workflow integration)</option>
+            </param>
+            <when value="text">
+                <param name="child_id" type="text"
+                       label="child sample ID in the VCF file" />
+                <param name="mother_id" type="text"
+                       label="Mother sample ID in the VCF file" />
+                <param name="father_id" type="text"
+                       label="Father sample ID in the VCF file" />
+            </when>
+            <when value="file">
+                <param name="child_id_file" type="data"
+                       label="Child sample ID in the VCF file. Provided as a single line file."/>
+                <param name="mother_id_file" type="data"
+                       label="Mother sample ID in the VCF file. Provided as a single line file."/>
+                <param name="father_id_file" type="data"
+                       label="Father sample ID in the VCF file. Provided as a single line file."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="tsv" name="updio_table" label="${tool.name} on ${output_label}: table"/>
+        <data format="tsv" name="updio_verdict" label="${tool.name} on ${output_label}: verdict"/>
+    </outputs>
+    <help><![CDATA[
+        UPDio is designed to detect UPD events in probands from vcf trio data.
+    ]]></help>
+</tool>
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