diff vardict.xml @ 0:2975b29bcaa1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vardict.xml	Tue Aug 25 05:41:19 2020 -0400
@@ -0,0 +1,176 @@
+<tool id="vardict_java" name="VarDict" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>calls SNVs and indels for tumor-normal pairs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
+        <requirement type="package" version="5.0.1">gawk</requirement>
+        <requirement type="package" version="1.10">samtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $select_mode.mode == "paired"
+            ln -s '$select_mode.normal' ./normal.bam &&
+            ln -s '$select_mode.normal.metadata.bam_index' ./normal.bam.bai &&
+        #end if
+        ln -s '$select_mode.tumor' ./tumor.bam &&
+        ln -s '$select_mode.tumor.metadata.bam_index' ./tumor.bam.bai &&
+
+        ## INDEX REFERENCE FASTA FILE IF FROM HISTORY
+        #if $reference_source.reference_source_selector == "history":
+            ln -s '$reference_source.ref_file' ./ref.fa &&
+            samtools faidx ./ref.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for vardict' >&2 &&
+        #else if $reference_source.reference_source_selector == "cached"
+            ln -s '$reference_source.ref_file.fields.path' ./ref.fa &&
+            ln -s '${reference_source.ref_file.fields.path}.fai' ./ref.fa.fai &&
+        #end if
+
+        ## build BED file from chromosome list
+        #if $interval_file:
+            grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai &&
+        #else
+            ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
+        #end if
+        awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' ./chromosomes.fa.fai > ./regions.bed &&
+
+        vardict-java
+        #if $select_mode.mode == "paired"
+            -b "./tumor.bam|./normal.bam"
+            -N 'Tumor'
+        #else
+            -b "./tumor.bam"
+            -N 'Sample'
+        #end if
+        -G ./ref.fa
+        -z
+        -th \${GALAXY_SLOTS:-1}
+
+        -f '$advancedsettings.f'
+        -k '$advancedsettings.k'
+        -r '$advancedsettings.r'
+        -B '$advancedsettings.B'
+        -Q '$advancedsettings.Q'
+        -q '$advancedsettings.q'
+        -m '$advancedsettings.m'
+        -T '$advancedsettings.T'
+        -X '$advancedsettings.X'
+        -P '$advancedsettings.P'
+        -o '$advancedsettings.o'
+        -O '$advancedsettings.O'
+        -V '$advancedsettings.V'
+
+        ## construct VFC table
+        -c 1 -S 2 -E 3 -g 4
+        ./regions.bed
+
+        ## postprocessing
+        #if $select_mode.mode == "paired"
+            | testsomatic.R
+            | var2vcf_paired.pl
+            -N 'Tumor|Normal'
+        #else
+            | teststrandbias.R
+            | var2vcf_valid.pl
+            -N 'Sample'
+            -E
+        #end if
+         -f '$advancedsettings.f'
+
+        > '$all_variants' &&
+
+        ## Filter for PASS variants
+        awk 'BEGIN {FS=OFS="\t"} substr(\$0, 1, 1) == "#" {print \$0; next} \$7 == "PASS" {print \$0}' '$all_variants' > '$passed_variants'
+    ]]></command>
+    <inputs>
+        <conditional name="select_mode">
+            <param name="mode" type="select" label="Choose run mode">
+                <option value="single">Single sample mode</option>
+                <option value="paired" selected="True">Paired variant calling</option>
+            </param>
+            <when value="single">
+                <expand macro="input_default" />
+            </when>
+            <when value="paired">
+                <param name="normal" type="data" format="bam" label="Normal file" />
+                <expand macro="input_default" />
+            </when>
+        </conditional>
+        <section name="advancedsettings" title="Advanced Settings" expanded="False">
+            <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum variant allele fraction" />
+            <param argument="-k" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Indicate whether to perform local realignment" />
+            <param argument="-r" type="integer" min="0" value="2" label="Minimum number of reads supporting the variant" />
+            <param argument="-B" type="integer" min="0" value="2" label="Minimum number of reads for determining strand bias" />
+            <param argument="-Q" type="integer" min="0" value="1" label="Minimum mapping quality for reads to be considered" />
+            <param argument="-m" type="integer" value="8" label="Maximum number of mismatches before a read is no longer considered (gaps are not counted as mismatches)" />
+            <param argument="-T" type="integer" value="0" label="Maximum number of bases considered from 5' end (default: 0, no trimming)" />
+            <param argument="-X" type="integer" value="3" label="Maximum number of extended based after indel to look for mismatches" />
+            <param argument="-P" type="integer" value="5" label="Maximum average read position for a variant to be considered." />
+            <param argument="-q" type="integer" value="25" label="Minimum phred score for a base to be considered a good call" />
+            <param argument="-o" type="float" value="1.5" label="Minimum quality ratio [(good_quality_reads)/(bad_quality_reads+0.5)] (based on definition of a good call; see previous option)" />
+            <param argument="-O" type="float" min="0" value="0" label="Minimum average mapping quality" />
+            <param argument="-V" type="float" min="0.0" max="1.0" value="0.05" label="Maximum allowed variant allele fraction in the normal sample" />
+        </section>
+        <expand macro="ref_select" />
+    </inputs>
+    <outputs>
+        <data name="all_variants" format="vcf" label="VarDict SNVs and Indels (All)" />
+        <data name="passed_variants" format="vcf" label="VarDict SNVs and Indels (Passed)" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <conditional name="select_mode">
+                <param name="mode" value="paired" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="tumor" ftype="bam" value="tumor.bam" />
+            </conditional>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="history"/>
+                <param name="ref_file" ftype="fasta" value="genome.fasta" />
+            </conditional>
+            <output name="all_variants" file="all_variants_paired.vcf" />
+            <output name="passed_variants" file="passed_variants_paired.vcf" />
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="select_mode">
+                <param name="mode" value="paired" />
+                <param name="normal" ftype="bam" value="normal.bam" />
+                <param name="tumor" ftype="bam" value="tumor.bam" />
+            </conditional>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="test_buildid"/>
+            </conditional>
+            <output name="all_variants" file="all_variants_paired.vcf" />
+            <output name="passed_variants" file="passed_variants_paired.vcf" />
+        </test>
+        <test expect_num_outputs="2">
+            <conditional name="select_mode">
+                <param name="mode" value="single" />
+                <param name="tumor" ftype="bam" value="tumor.bam" />
+            </conditional>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="test_buildid"/>
+            </conditional>
+            <output name="all_variants" file="all_variants_single.vcf" />
+            <output name="passed_variants" file="passed_variants_single.vcf" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
+VarDict
+=======
+
+VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files.
+VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments,
+rescue of long indels by realigning bwa soft clipped reads and better scalability than many other Java based variant callers.
+
+For more information see the VarDict documentation_.
+
+.. _documentation: https://github.com/AstraZeneca-NGS/VarDictJava
+        ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkw227</citation>
+    </citations>
+</tool>