# HG changeset patch
# User ftouzain
# Date 1687448519 0
# Node ID 921286a54e950075990dbb5a3643876585d01188

Uploaded wrapper for vcutils.pl vcf2fq

diff -r 000000000000 -r 921286a54e95 vcfutils_vcf2fq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfutils_vcf2fq.xml	Thu Jun 22 15:41:59 2023 +0000
@@ -0,0 +1,52 @@
+<tool id="vcfutils_vcf2fq" name="vcfutils_vcf2fq: convert vcf file to fastq file" version="1.16" python_template_version="3.9">
+    <requirements>
+      <requirement type="package" version="1.16">bcftools</requirement>	      
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+       vcfutils.pl vcf2fq -d '$min_depth' -D '$max_depth' -Q '$min_RMS_mapQ' -l '$filtering_window' '$all_sites_vcf_f' > '$fastq_f'
+    ]]></command>
+    <inputs>
+      <param type="data" name="all_sites_vcf_f" format="vcf" />
+      <param type="integer" name="min_depth" label="min covereage depth" value="3" />
+      <param type="integer" name="max_depth" label="max coverage depth" value="100000" />
+      <param type="integer" name="min_RMS_mapQ" label="min RMS mapQ" value="10" />
+      <param type="integer" name="filtering_window" label="filtering window" value="5" />
+    </inputs>
+    <outputs>
+        <data name="fastq_f" format="fastq" />
+    </outputs>
+    <tests>
+      <test>
+            <param name="all_sites_vcf_f" value="test_vcfutils_vcf2fq/all_sites.vcf"/>	
+            <output name="fastq_f" file="test_vcfutils_vcf2fq/consensus.fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+[vcfutils_vcf2fq]
+Aim: Deduce from vcf file output fastq file
+in:
+- vcf file with all sites
+out:
+- consensus fastq file
+
+usage: vcfutils.pl vcf2fq all_sites.vcf > consensus.fastq
+
+optional arguments:
+  -d INT minimum depth [3]
+  -D INT maximum depth [100000]
+  -Q INT min RMS mapQ  [10]
+  -l INT INDEL filtering window [5]
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{vcfutils_vcf2fq,
+  author = {Li, Heng},
+  year = {2009},
+  title = {The Sequence Alignment/Map format and SAMtools},
+  publisher = {},
+  journal = {Bioinformatics},
+  url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002},
+	}</citation>
+      <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
+</tool>