# HG changeset patch
# User sanbi-uwc
# Date 1617833220 0
# Node ID 499b71c93c5d2a97be4ed3b38d8970e697f90654
# Parent  e34ab51fa707948640c23ce476229e4fd8ef0eb1
"planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/qc commit c11a408ecf1ea81fcca4bac8d503ee2731077722-dirty"

diff -r e34ab51fa707 -r 499b71c93c5d qc.xml
--- a/qc.xml	Thu Apr 01 07:57:59 2021 +0000
+++ b/qc.xml	Wed Apr 07 22:07:00 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="qc_cog_uk" name="Quality Control (COG-UK QC)" version="0.1.0" python_template_version="3.5">
+<tool id="qc_cog_uk" name="Quality Control (COG-UK QC)" version="0.1.1" python_template_version="3.5">
     <requirements>
         <requirement type="package" version="1.11">samtools</requirement>
         <requirement type="package" version="1.78">biopython</requirement>
@@ -8,25 +8,13 @@
     <command detect_errors="exit_code" interpreter="python"><![CDATA[
         qc.py '$qc_type_conditional.qc_type' 
             --outfile '$output1' 
-            --sample '$input_sample'
+            --sample 'sample'
             --ref '$input_ref' 
             --bam '$input_bam' 
             --fasta '$input_cons_fasta' && 
-        mv '$input_sample'.depth.png '$output2'
+        mv sample.depth.png '$output2'
     ]]></command>
     <inputs>
-        <conditional name="input_type_conditional">
-            <param name="input_type" type="select" label="Input Type">
-                <option value="single" selected="true">Single Dataset</option>
-                <option value="paired_collection">Paired Collection</option>
-            </param>
-            <when value="single">
-                 <param name="input_sample" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
-            </when>
-            <when value="paired_collection">
-                 <param name="input_sample" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
-            </when>
-        </conditional>
         <conditional name="qc_type_conditional">
             <param name="qc_type" type="select" label="Input Type">
                 <option value="--illumina" selected="true">Illumina</option>