changeset 7:7d5b46d41ff0 draft

Uploaded

--- a/bcbio-nextgen.xml	Thu Feb 27 14:25:51 2020 +0000
+++ b/bcbio-nextgen.xml	Tue Apr 21 11:38:25 2020 +0000
@@ -8,7 +8,11 @@
           --bed ${region_file.bed} 
         #end if
         #for $i, $sample in enumerate( $samples )
-            --input $sample.forward:$sample.reverse:$sample.phenotype
+            #if str( $sample.single_or_paired.single_or_paired_selector ) == "single":
+                --input $sample.single_or_paired.forward:$sample.phenotype
+            #else:
+                --input $sample.single_or_paired.forward:$sample.single_or_paired.reverse:$sample.phenotype
+            #end if
         #end for
         && bcbio_nextgen.py \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml -t local -n \$BCBIO_CORES && 
         zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf &&
@@ -30,7 +34,11 @@
   analysis: $analysis
   lane: {{ loop.index }}
   description: {{ sample['description'] }}
+{% if 'reverse' in sample %}
   files: [{{ sample['forward'] }}, {{ sample['reverse'] }}]
+{% else %}
+  files: [{{ sample['forward'] }}]
+{% endif %}
   genome_build: $build
   metadata:
     phenotype: {{ sample['phenotype'] }}
@@ -93,8 +101,19 @@
                 <option value="normal">Normal</option>
                 <option value="tumor">Tumor</option>
             </param>
-            <param type="data" name="forward" format="fastq,fastq.gz,fastqsanger.gz" />
-            <param type="data" name="reverse" format="fastq,fastq.gz,fastqsanger.gz" />
+            <conditional name="single_or_paired">
+                <param name="single_or_paired_selector" type="select">
+                    <option value="single">Single</option>
+                    <option value="paired" selected="true">Paired-End</option>
+                </param>
+                <when value="single">
+                    <param type="data" name="forward" format="fastq,fastq.gz,fastqsanger.gz" />
+                </when>
+                <when value="paired">
+                    <param type="data" name="forward" format="fastq,fastq.gz,fastqsanger.gz" />
+                    <param type="data" name="reverse" format="fastq,fastq.gz,fastqsanger.gz" />
+                </when>
+            </conditional>
         </repeat>
         <conditional name="region_file">
             <param name="has_region_file_select" type="select" label="Do you have a region file">
@@ -113,4 +132,4 @@
     <help><![CDATA[
         TODO: Fill in help.
     ]]></help>
-</tool>
\ No newline at end of file
+</tool>