diff fermikit_run_calling.xml @ 0:44519e762f16 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fermikit_run_calling.xml	Thu Jan 05 08:35:48 2017 -0500
@@ -0,0 +1,58 @@
+<tool id="fermikit_variants" name="fermikit-variants" version="0.14.dev1">
+    <description>call variants from genome-aligned contigs</description>
+    <requirements>
+        <requirement type="package" version="0.14.dev1">fermikit</requirement>
+        <requirement type="package" version="0.6.5">sambamba</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        #import re
+        #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($bam.element_identifier))
+        #set ref = $reference_genome.fasta_item.fields.path if $reference_genome.reference_genome_source == "reference" else $reference_genome.history_item
+        export ROOT=\$(dirname \$(type -P k8)) &&
+        ln -f -s '$bam' '$escaped_element_identifier' &&
+        htsbox pileup -cuf '$ref' '$escaped_element_identifier'  | gzip -1 > raw.vcf.gz &&
+        k8 "\$ROOT"/hapdip.js deovlp raw.vcf.gz | k8 "\$ROOT"/hapdip.js anno | gzip -1 > tmp.vcf.gz 2> flt.vcf.log &&
+        k8 "\$ROOT"/hapdip.js filter -q3 tmp.vcf.gz > flt.vcf 2>> flt.vcf.log &&
+        htsbox abreak -bcuf '$ref' <(sambamba sort -n -o /dev/stdout '$escaped_element_identifier') > sv.vcf
+     ]]></command>
+     <inputs>
+         <param name="bam" type="data" label="aligned contigs" help="To generate aligned contigs align fermi2 contigs with BWA mem options -B9 -O16 -L5" format="bam"/>
+         <conditional name="reference_genome" label="Reference genome to call variants against">
+             <param name="reference_genome_source" type="select">
+                 <option value="reference">Use a built-in genome to call variants</option>
+                 <option value="history">Use a genome from history to call variants</option>
+             </param>
+             <when value="history">
+                <param format="fasta" label="Select a reference genome" name="history_item" type="data" />
+            </when>
+            <when value="reference">
+                <param label="Select a reference genome" name="fasta_item" type="select">
+                    <options from_data_table="all_fasta">
+                        <filter column="2" type="sort_by"/>
+                    </options>
+                </param>
+            </when>
+         </conditional>
+    </inputs>
+    <outputs>
+        <data name="structural_variants" format="vcf" label="fermikit SV on ${on_string}" from_work_dir="sv.vcf"/>
+        <data name="snps_indels" format="vcf" label="fermikit SNPs and short INDELs on ${on_string}" from_work_dir="flt.vcf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference_genome_source" value="history"/>
+            <param name="history_item" value="small.fa.gz" ftype="fasta"/>
+            <param name="bam" value="aligned_contigs.bam"/>
+            <output name="structural_variants" file="sv.vcf" lines_diff="2"/>
+            <output name="snps_indels" file="flt.vcf" lines_diff="2"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+FermiKit is a de novo assembly based variant calling pipeline for deep Illumina
+resequencing data. This galaxy wrapper can be used to call variants from contigs
+generated by fermi2 that have subsequently been aligned to a reference genome
+using bwa (options -B9 -O16 -L5 or -x intractg).
+
+]]></help> <citations> <citation
+type="doi">10.1093/bioinformatics/btv440</citation> </citations> </tool>