Mercurial > repos > morinlab > vardictjava
diff vardictjava.xml @ 0:fba18d3160d1 draft default tip
planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/vardictjava commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
| author | morinlab |
|---|---|
| date | Tue, 11 Oct 2016 14:37:45 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vardictjava.xml Tue Oct 11 14:37:45 2016 -0400 @@ -0,0 +1,129 @@ +<tool id="vardictjava" name="VarDictJava" version="1.4.6"> + <description> + calls SNVs and indels for tumour-normal pairs. + </description> + + <requirements> + <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.4.6">vardictjava</requirement> + <requirement type="set_environment">VARDICTJAVA_ROOT_DIR</requirement> + </requirements> + + <command detect_errors="aggressive"><![CDATA[ + ## LINK BAM INDEX + ln -s $normal ./normal.bam; + ln -s $normal.metadata.bam_index ./normal.bam.bai; + ln -s $tumour tumor.bam; + ln -s $tumour.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; + #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; + + ## BUILD VARDICT COMMAND + \$VARDICTJAVA_ROOT_DIR/build/install/VarDict/bin/VarDict + -b "./tumor.bam|./normal.bam" + -G ref.fa + -z + -th \${GALAXY_SLOTS:-1} + + ## ADVANCED OPTIONS + -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 VCF TABLE + -c 1 -S 2 -E 3 -g 4 + + ## REGION SPECIFICATION (ENTIRE CHROMOSOMES) + regions.bed + + ## POSTPROCESSING + | \$VARDICTJAVA_ROOT_DIR/VarDict/testsomatic.R + | \$VARDICTJAVA_ROOT_DIR/VarDict/var2vcf_somatic.pl + -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="reference_source"> + <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file"> + <option value="cached" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from the history</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Reference Genome File"> + <options from_data_table="fasta_indexes"/> + </param> + </when> + <when value="history"> + <param name="ref_file" format="fasta" type="data" label="Reference Genome File" /> + </when> + </conditional> + + <param name="normal" type="data" format="bam" label="Normal Alignment File" /> + <param name="tumour" type="data" format="bam" label="Tumour Alignment File" /> + <param name="interval_file" type="data" format="txt" optional="true" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" /> + + <section name="advancedsettings" title="Advanced Settings" expanded="False"> + <param name="f" type="float" value="0.01" label="Minimum variant allele fraction" /> + <param name="k" type="integer" value="1" label="Set to 0 to disable local realignment" /> + <param name="r" type="integer" value="2" label="Minimum number of reads supporting the variant" /> + <param name="B" type="integer" value="2" label="Minimum number of reads for determining strand bias" /> + <param name="Q" type="integer" value="1" label="Minimum mapping quality for reads to be considered" /> + <param name="m" type="integer" value="8" label="Maximum number of mismatches before a read is no longer considered (gaps are not counted as mismatches)" /> + <param name="T" type="integer" value="0" label="Maximum number of bases considered from 5' end (default: 0, no trimming)" /> + <param name="X" type="integer" value="3" label="Maximum number of extended based after indel to look for mismatches" /> + <param name="P" type="integer" value="5" label="Maximum average read position for a variant to be considered." /> + <param name="q" type="integer" value="25" label="Minimum phred score for a base to be considered a good call" /> + <param name="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 name="O" type="float" value="0" label="Minimum average mapping quality" /> + <param name="V" type="float" value="0.05" label="Maximum allowed variant allele fraction in the normal sample" /> + </section> + </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> + + <help> + <![CDATA[ + https://github.com/AstraZeneca-NGS/VarDictJava + ]]> + </help> + + <citations> + <expand macro="morinlab_citation" /> + <expand macro="galaxy_citation" /> + <expand macro="vardict_citation" /> + </citations> +</tool>