varscan_somatic: varscan_somatic.xml annotate

annotate varscan_somatic.xml @ 7:2ea345eef4e2 draft

"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156"

author	iuc
date	Fri, 16 Aug 2019 15:48:18 -0400
parents	def508f3149e
children	485ea638e0ca

rev	line source
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	1 <tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.5">
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	2 <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	3 <macros>
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	4 <import>macros.xml</import>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	5 <macro name="test_mentions_contig">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	6 <assert_contents>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	7 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	8 expression="##contig=.ID=chrM,length=16571." />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	9 </assert_contents>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	10 </macro>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	11 <macro name="test_mentions_filters">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	12 <assert_contents>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	13 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	14 expression="##FILTER=.ID=VarCount,Description=.+" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	15 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	16 expression="##FILTER=.ID=ReadLenDiff,Description=.+" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	17 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	18 expression="##FILTER=.ID=RefDist3,Description=.+" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	19 </assert_contents>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	20 </macro>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	21 <macro name="test_not_mentions_filters">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	22 <assert_contents>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	23 <not_has_text
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	24 text="##FILTER=<ID=VarCount,Description=" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	25 <not_has_text
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	26 text="##FILTER=<ID=ReadLenDiff,Description=" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	27 <not_has_text
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	28 text="##FILTER=<ID=RefDist3,Description=" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	29 </assert_contents>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	30 </macro>
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	31 <macro name="filter_compat_options">
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	32 <section name="experts_only" title="Compatibility options for experts" expanded="false">
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	33 <param name="compat_opts" type="select" display="checkboxes" multiple="true" optional="true"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	34 label="Compatibility Options for Posterior Variant Filtering"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	35 help="">
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	36 <option value="--ignore-md" selected="true">Always determine mismatch quality statistics from recalculated read to reference alignments. Ignore read MD tags if present.</option>
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	37 <option value="--detect-q2-runs" selected="false">Treat runs of base qualities of value 2 at the 3' end of reads as quality control indicator (Illumina 1.5 compatibility setting)</option>
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	38 </param>
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	39 </section>
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	40 </macro>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	41 </macros>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	42 <expand macro="requirements">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	43 <requirement type="package" version="3.6.7">python</requirement>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	44 <requirement type="package" version="0.15.1">pysam</requirement>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	45 </expand>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	46 <stdio>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	47 <exit_code range="1:" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	48 </stdio>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	49 <command><![CDATA[
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	50 #if str($reference.source) == "history":
3 1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	51 #set $ref_genome = 'ref.fa'
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	52 ln -s -f '$reference.genome' $ref_genome &&
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	53 #else:
3 1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	54 #set $ref_genome = str($reference.genome.fields.path)
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	55 #end if
3 1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	56 #set $normal_data = 'normal.bam'
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	57 #set $tumor_data = 'tumor.bam'
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	58 ln -s -f '$normal_bam' $normal_data &&
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	59 ln -s -f '$tumor_bam' $tumor_data &&
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	60 ln -s -f '${normal_bam.metadata.bam_index}' ${normal_data}.bai &&
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	61 ln -s -f '${tumor_bam.metadata.bam_index}' ${tumor_data}.bai &&
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	62 python3 $__tool_directory__/varscan.py
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	63 --normal '$normal_data'
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	64 --tumor '$tumor_data'
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	65 --normal-purity ${normal_purity}
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	66 --tumor-purity ${tumor_purity}
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	67 #if str($split_output):
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	68 --ofile variants_out
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	69 $split_output
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	70 #else:
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	71 --ofile '$output'
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	72 #end if
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	73 --threads \${GALAXY_SLOTS:-2}
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	74 #if str($call_params.settings) == "custom":
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	75 ## samtools mpileup parameters
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	76 --min-basequal ${call_params.read_selection.min_basequal}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	77 --min-mapqual ${call_params.read_selection.min_mapqual}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	78 ${call_params.read_selection.count_orphans}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	79 ${call_params.read_selection.detect_overlaps}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	80 --max-pileup-depth ${call_params.read_selection.max_pileup_depth}
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	81 ## VarScan parameters
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	82 --min-coverage ${call_params.min_coverage}
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	83 --min-var-count ${call_params.min_reads2}
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	84 --min-var-freq ${call_params.min_var_freq}
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	85 --min-hom-freq ${call_params.min_freq_for_hom}
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	86 --p-value ${call_params.p_value}
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	87 --somatic-p-value ${call_params.somatic_p_value}
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	88 #end if
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	89 #if str($filter_params.settings) == "no_filter":
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	90 --no-filters
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	91 #else:
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	92 #if str($filter_params.settings) == "dream3_settings":
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	93 --min-var-count2 3
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	94 --min-var-count2-lc 1
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	95 --min-var-count2-depth 10
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	96 --min-var-freq2 0.05
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	97 --min-ref-readpos 0.2
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	98 --min-var-readpos 0.15
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	99 --min-ref-dist3 0.2
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	100 --min-var-dist3 0.15
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	101 --min-ref-len 90
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	102 --min-var-len 90
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	103 --max-len-diff 0.05
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	104 --min-strandedness 0
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	105 --min-strand-reads 5
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	106 --min-ref-basequal 15
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	107 --min-var-basequal 30
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	108 --max-basequal-diff 50
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	109 --min-ref-mapqual 20
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	110 --min-var-mapqual 30
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	111 --max-mapqual-diff 10
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	112 --max-ref-mmqs 50
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	113 --max-var-mmqs 100
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	114 --min-mmqs-diff 0
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	115 --max-mmqs-diff 50
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	116 #elif str($filter_params.settings) == "custom":
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	117 --min-var-count2 ${filter_params.min_var_count}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	118 --min-var-count2-lc ${filter_params.min_var_count_lc}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	119 --min-var-count2-depth ${filter_params.min_var_count_depth}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	120 --min-var-freq2 ${filter_params.min_var_freq2}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	121 --min-ref-readpos ${filter_params.min_ref_readpos}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	122 --min-var-readpos ${filter_params.min_var_readpos}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	123 --min-ref-dist3 ${filter_params.min_ref_dist3}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	124 --min-var-dist3 ${filter_params.min_var_dist3}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	125 --min-ref-len ${filter_params.min_ref_len}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	126 --min-var-len ${filter_params.min_var_len}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	127 --max-len-diff ${filter_params.max_len_diff}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	128 --min-strandedness ${filter_params.min_strandedness}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	129 --min-strand-reads ${filter_params.min_strand_reads}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	130 --min-ref-basequal ${filter_params.min_ref_basequal}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	131 --min-var-basequal ${filter_params.min_var_basequal}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	132 --max-basequal-diff ${filter_params.max_basequal_diff}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	133 --min-ref-mapqual ${filter_params.min_ref_mapqual}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	134 --min-var-mapqual ${filter_params.min_var_mapqual}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	135 --max-mapqual-diff ${filter_params.max_mapqual_diff}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	136 --max-ref-mmqs ${filter_params.max_ref_mmqs}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	137 --max-var-mmqs ${filter_params.max_var_mmqs}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	138 --min-mmqs-diff ${filter_params.min_mmqs_diff}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	139 --max-mmqs-diff ${filter_params.max_mmqs_diff}
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	140 #end if
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	141 #if $filter_params.experts_only.compat_opts:
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	142 #for $opt in str($filter_params.experts_only.compat_opts).split(','):
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	143 $opt
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	144 #end for
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	145 #end if
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	146 #end if
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	147 --verbose
3 1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	148 '$ref_genome'
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	149 ]]></command>
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	150
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	151 <inputs>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	152 <conditional name="reference">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	153 <param name="source" type="select"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	154 label="Will you select a reference genome from your history or use a built-in genome?">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	155 <option value="cached">Use a built-in genome</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	156 <option value="history">Use a genome from my history</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	157 </param>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	158 <when value="cached">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	159 <param name="genome" type="select"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	160 label="reference genome"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	161 help="The fasta reference genome that variants should be called against.">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	162 <options from_data_table="fasta_indexes" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	163 </param>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	164 </when>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	165 <when value="history">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	166 <param name="genome" type="data" format="fasta"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	167 label="reference genome"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	168 help="The fasta reference genome that variants should be called against."/>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	169 </when>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	170 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	171 <param name="normal_bam" type="data" format="bam"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	172 label="aligned reads from normal sample" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	173 <param name="tumor_bam" type="data" format="bam"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	174 label="aligned reads from tumor sample" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	175 <param argument="--normal-purity" name="normal_purity" type="float" value="1.0" min="0" max="1.0"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	176 label="Estimated purity (non-tumor content) of normal sample"/>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	177 <param argument="--tumor-purity" name="tumor_purity" type="float" value="1.0" min="0" max="1.0"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	178 label="Estimated purity (tumor content) of tumor sample"/>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	179 <param name="split_output" type="boolean" truevalue="--split-output" falsevalue="" checked="false"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	180 label="Generate separate output datasets for SNP and indel calls?" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	181 <conditional name="call_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	182 <param name="settings" label="Settings for Variant Calling" type="select">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	183 <option value="varscan_defaults" selected="true">Use default values</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	184 <option value="custom">Customize settings</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	185 </param>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	186 <when value="custom">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	187 <section name="read_selection" title="Read selection" expanded="true"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	188 help="The settings in this section control which mapped reads will be used for variant calling.">
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	189 <param argument="samtools mpileup -Q" name="min_basequal" type="integer" value="13" min="1" max="50"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	190 label="Minimum base quality"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	191 help="The minimum base quality (default: 13) at a given position required to use a read for calling variants at that site" />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	192 <param argument="samtools mpileup -q" name="min_mapqual" type="integer" value="0" min="0" max="60"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	193 label="Minimum mapping quality"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	194 help="The minimum mapping quality (default: 0) required for a read to be considered in variant calling" />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	195 <param argument="samtools mpileup -A" name="count_orphans" type="boolean" truevalue="--count-orphans" falsevalue="" checked="false"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	196 label="Use reads from anomalously mapped pairs"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	197 help="Applies to paired-end reads only. If set to true, reads from pairs that are flagged as non-proper pairs (SAM/BAM FLAG field 2) will be used in variant calling. The default is to ignore such reads." />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	198 <param argument="samtools mpileup -x" name="detect_overlaps" type="boolean" truevalue="" falsevalue="--no-detect-overlaps" checked="true"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	199 label="Try to correct for read-pair overlaps"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	200 help="Applies to paired-end reads only. If the reads of a pair overlap on the reference, then with this option (on by default), the bases for which both reads provide evidence will be counted only once in variant calling (of the two sequenced bases in the reads, the base with the better base quality will be used)." />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	201 <param argument="samtools mpileup -d" name="max_pileup_depth" type="integer" value="8000" min="4000"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	202 label="Maximum number of reads per site"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	203 help="Restrict the number of reads used for variant calling at a site to this maximum (default: 8000) for each sample. Helps protect against excessive memory usage (and slow tool runs) at sites of extraordinary high coverage." />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	204 </section>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	205 <expand macro="min_coverage"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	206 help="Minimum site coverage (default: 8) required in the normal and in the tumor sample to call a variant. This threshold gets applied after eliminating reads based on the read selection criteria above." />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	207 <expand macro="min_reads2"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	208 help="Minimum number (default: 2) of variant-supporting reads (after read selection) at a position required to make a call"/>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	209 <expand macro="min_var_freq" value="0.1" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	210 <expand macro="min_freq_for_hom" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	211 <expand macro="p_value" value="0.99"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	212 help="The p-value threshold (default: 0.99) used to determine if a variant should be called for either sample" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	213 <param argument="--somatic-p-value" name="somatic_p_value" type="float" value="0.05" min="0" max="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	214 label="P-value threshold for calling somatic variants and LOH events"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	215 help="The p-value threshold (default: 0.05) used to determine if read count differences between the normal and the tumor sample justify classification of a variant as somatic or as an LOH event" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	216 </when>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	217 <when value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	218 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	219 <conditional name="filter_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	220 <param name="settings" label="Settings for Posterior Variant Filtering" type="select">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	221 <option value="varscan_defaults" selected="true">Use default values</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	222 <option value="dream3_settings">Use settings optimized for DREAM-3</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	223 <option value="no_filter">Do not perform posterior filtering</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	224 <option value="custom">Customize settings</option>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	225 </param>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	226 <when value="no_filter" />
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	227 <when value="varscan_defaults">
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	228 <expand macro="filter_compat_options" />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	229 </when>
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	230 <when value="dream3_settings">
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	231 <expand macro="filter_compat_options" />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	232 </when>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	233 <when value="custom">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	234 <param argument="--min-var-count" name="min_var_count" type="integer" value="4" min="1" max="200"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	235 label="Minimum number of variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	236 help="(default: 4)" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	237 <param argument="--min-var-count-lc" name="min_var_count_lc" type="integer" value="2" min="1" max="200"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	238 label="Low coverage minimum number of variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	239 help="This setting (default: 2) will be applied instead of the --min-var-count limit for sites with poor overall (see threshold below) coverage." />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	240 <param argument="--max-somatic-p-depth" name="min_var_count_depth" type="integer" value="10" min="2" max="200"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	241 label="Minimum variant allele count threshold"
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	242 help="Combined depth (default: 10) of ref- and variant-supporting reads required at variant site to apply the (stricter) --min-var-count filter instead of --min-var-count-lc" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	243 <param argument="--min-var-freq" name="min_var_freq2" type="float" value="0.05" min="0" max="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	244 label="Minimum variant allele frequency"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	245 help="(default: 0.05)" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	246 <param argument="--min-ref-readpos" name="min_ref_readpos" type="float" value="0.1" min="0" max="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	247 label="Minimum relative variant position in ref-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	248 help="The minimum average relative distance from either end of ref-supporting reads (default: 0.1) required for variant sites" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	249 <param argument="--min-var-readpos" name="min_var_readpos" type="float" value="0.1" min="0" max="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	250 label="Minimum relative variant position in variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	251 help="The minimum average relative distance from either end of variant-supporting reads (default: 0.1) required for variant sites" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	252 <param argument="--min-ref-dist3" name="min_ref_dist3" type="float" value="0.1" min="0" max="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	253 label="Minimum distance of variant site from 3'-end of ref-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	254 help="The minimum average relative distance from the effective 3'end of ref-supporting reads (default: 0.1) required for variant sites. The effective 3'end is defined by the end of the alignment of the read to the reference (or, if the Illumina 1.5 compatibility setting is used, by the first base in 3'->5' direction with a base quality > 2)." />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	255 <param argument="--min-var-dist3" name="min_var_dist3" type="float" value="0.1" min="0" max="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	256 label="Minimum distance of variant site from 3'-end of variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	257 help="The minimum average relative distance from the effective 3'end of variant-supporting reads (default: 0.1) required for variant sites. The effective 3'end is defined as above." />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	258 <param argument="--min-ref-avgrl" name="min_ref_len" type="integer" value="90" min="0" max="200"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	259 label="Minimum length of ref-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	260 help="The minimum average trimmed length (default: 90) required for reads supporting the reference allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	261 <param argument="--min-var-avgrl" name="min_var_len" type="integer" value="90" min="0" max="200"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	262 label="Minimum length of variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	263 help="The minimum average trimmed length (default: 90) required for reads supporting the variant allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	264 <param argument="--max-rl-diff" name="max_len_diff" type="float" value="0.25" min="0" max="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	265 label="Maximum relative read length difference"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	266 help="The maximum allowed difference (default: 0.25) in the average relative read length (ref - var) between reads supporting the reference and the variant allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	267 <param argument="--min-strandedness" name="min_strandedness" type="float" value="0.01" min="0" max="0.5"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	268 label="Minimum fraction of variant reads from each strand"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	269 help="The minimum fraction (default: 0.01) of variant reads that are required to come from the forward and from the reverse strand" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	270 <param argument="--min-strand-reads" name="min_strand_reads" type="integer" value="5" min="2" max="200"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	271 label="Minimum variant allele depth required to apply the --min-strandedness filter"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	272 help="(default: 5)" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	273 <param argument="--min-ref-basequal" name="min_ref_basequal" type="integer" value="15" min="1" max="50"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	274 label="Minimum average base quality for the ref allele"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	275 help="The minimum average base quality (default: 15) required at the variant site for reads supporting the reference allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	276 <param argument="--min-var-basequal" name="min_var_basequal" type="integer" value="15" min="1" max="50"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	277 label="Minimum average base quality for the variant allele"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	278 help="The minimum average base quality (default: 15) required at the variant site for reads supporting the variant allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	279 <param argument="max-basequal-diff" name="max_basequal_diff" type="integer" value="50" min="0" max="50"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	280 label="Maximum base quality difference between ref- and variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	281 help="The maximum difference (default: 50) in the average base quality (ref - var) allowed between the variant site positions of reads supporting the reference and the variant allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	282 <param argument="--min-ref-mapqual" name="min_ref_mapqual" type="integer" value="15" min="1" max="60"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	283 label="Minimum average mapping quality of ref-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	284 help="The minimum average mapping quality (default: 15) required for reads supporting the reference allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	285 <param argument="--min-var-mapqual" name="min_var_mapqual" type="integer" value="15" min="1" max="60"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	286 label="Minimum average mapping quality of variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	287 help="The minimum average mapping quality (default: 15) required for reads supporting the variant allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	288 <param argument="--max-mapqual-diff" name="max_mapqual_diff" type="integer" value="50" min="0" max="60"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	289 label="Maximum mapping quality difference between ref- and variant-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	290 help="The maximum difference (default: 50) in the average mapping quality (ref - var) allowed between reads supporting the reference and the variant allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	291 <param argument="--max-ref-mmqs" name="max_ref_mmqs" type="integer" value="100" min="0"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	292 label="Maximum mismatch base quality sum of ref-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	293 help="The maximum mismatch base quality sum (default: 100) allowed for reads supporting the reference allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	294 <param argument="--max-var-mmqs" name="max_var_mmqs" type="integer" value="100" min="0"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	295 label="Maximum mismatch base quality sum of var-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	296 help="The maximum mismatch base quality sum (default: 100) allowed for reads supporting the variant allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	297 <param argument="--min-mmqs-diff" name="min_mmqs_diff" type="integer" value="0" min="0"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	298 label="Minimum difference between mismatch base quality sums of variant- and ref-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	299 help="The minimum difference (default: 0) in the mismatch base quality sums (var - ref) required between reads supporting the variant and the reference allele" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	300 <param argument="--max-mmqs-diff" name="max_mmqs_diff" type="integer" value="50" min="1"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	301 label="Maximum difference between mismatch base quality sums of variant- and ref-supporting reads"
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	302 help="The maximum difference (default: 50) in the mismatch base quality sums (var - ref) allowed between reads supporting the variant and the reference allele" />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	303 <expand macro="filter_compat_options" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	304 </when>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	305 </conditional>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	306 </inputs>
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	307 <outputs>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	308 <data name="output" format="vcf">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	309 <filter>not split_output</filter>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	310 </data>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	311 <data name="output_snp" from_work_dir="variants_out.snp" format="vcf"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	312 label="Varscan somatic SNP calls on ${on_string}">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	313 <filter>split_output</filter>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	314 </data>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	315 <data name="output_indel" from_work_dir="variants_out.indel" format="vcf"
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	316 label="Varscan somatic indel calls on ${on_string}">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	317 <filter>split_output</filter>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	318 </data>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	319 </outputs>
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	320 <tests>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	321 <test expect_num_outputs="1">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	322 <!-- run with default settings and genome from history -->
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	323 <conditional name="reference">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	324 <param name="source" value="history" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	325 <param name="genome" value="hg19_chrM.fa" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	326 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	327 <param name="normal_bam" value="control_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	328 <param name="tumor_bam" value="tumor_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	329 <param name="split_output" value="false" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	330 <conditional name="call_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	331 <param name="settings" value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	332 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	333 <conditional name="filter_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	334 <param name="settings" value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	335 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	336 <output name="output">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	337 <expand macro="test_mentions_contig" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	338 <expand macro="test_mentions_filters" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	339 </output>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	340 </test>
3 1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	341 <test expect_num_outputs="1">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	342 <!-- run with default settings and cached genome -->
3 1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	343 <conditional name="reference">
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	344 <param name="source" value="cached" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	345 <param name="genome" value="hg19mito" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	346 </conditional>
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	347 <param name="normal_bam" dbkey="hg19" value="control_chrM.bam" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	348 <param name="tumor_bam" dbkey="hg19" value="tumor_chrM.bam" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	349 <param name="split_output" value="false" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	350 <conditional name="call_params">
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	351 <param name="settings" value="varscan_defaults" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	352 </conditional>
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	353 <conditional name="filter_params">
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	354 <param name="settings" value="varscan_defaults" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	355 </conditional>
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	356 <output name="output">
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	357 <expand macro="test_mentions_contig" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	358 <expand macro="test_mentions_filters" />
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	359 </output>
1f4bc80bd40c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934 iuc parents: 2 diff changeset	360 </test>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	361 <test expect_num_outputs="2">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	362 <!-- run with default settings and split output -->
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	363 <conditional name="reference">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	364 <param name="source" value="history" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	365 <param name="genome" value="hg19_chrM.fa" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	366 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	367 <param name="normal_bam" value="control_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	368 <param name="tumor_bam" value="tumor_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	369 <param name="split_output" value="true" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	370 <conditional name="call_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	371 <param name="settings" value="varscan_defaults" />
1 fd901d18b081 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177 iuc parents: 0 diff changeset	372 </conditional>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	373 <conditional name="filter_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	374 <param name="settings" value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	375 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	376 <output name="output_indel">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	377 <expand macro="test_mentions_contig" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	378 <expand macro="test_mentions_filters" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	379 </output>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	380 <output name="output_snp">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	381 <expand macro="test_mentions_contig" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	382 <expand macro="test_mentions_filters" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	383 </output>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	384 </test>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	385 <test expect_num_outputs="1">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	386 <!-- run with custom params for variant calling -->
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	387 <conditional name="reference">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	388 <param name="source" value="history" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	389 <param name="genome" value="hg19_chrM.fa" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	390 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	391 <param name="normal_bam" value="control_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	392 <param name="tumor_bam" value="tumor_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	393 <param name="split_output" value="false" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	394 <conditional name="call_params">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	395 <section name="read_selection">
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	396 <param name="min_basequal" value="5" />
2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	397 </section>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	398 <param name="settings" value="custom" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	399 <param name="min_coverage" value="2" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	400 <param name="min_reads2" value="1" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	401 <param name="min_var_freq" value="0.01" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	402 <param name="min_freq_for_hom" value="0.66" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	403 <param name="p_value" value="0.97" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	404 <param name="somatic_p_value" value="0.09" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	405 </conditional>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	406 <param name="normal_purity" value="0.6" />
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	407 <param name="tumor_purity" value="0.6" />
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	408 <conditional name="filter_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	409 <param name="settings" value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	410 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	411 <assert_stderr>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	412 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	413 expression=" Min coverage: 2x for Normal, 2x for Tumor" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	414 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	415 expression="Min reads2: 1" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	416 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	417 expression="Min var freq: 0.01" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	418 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	419 expression="Min freq for hom: 0.66" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	420 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	421 expression="Normal purity: 0.6" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	422 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	423 expression="Tumor purity: 0.6" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	424 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	425 expression="Min avg qual: 5" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	426 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	427 expression="P-value thresh: 0.97" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	428 <has_line_matching
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	429 expression="Somatic p-value: 0.09" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	430 </assert_stderr>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	431 <output name="output">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	432 <expand macro="test_mentions_contig" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	433 <expand macro="test_mentions_filters" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	434 </output>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	435 </test>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	436 <test expect_num_outputs="1">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	437 <!-- run with preconfigured dream3 post-filter settings -->
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	438 <conditional name="reference">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	439 <param name="source" value="history" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	440 <param name="genome" value="hg19_chrM.fa" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	441 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	442 <param name="normal_bam" value="control_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	443 <param name="tumor_bam" value="tumor_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	444 <param name="split_output" value="false" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	445 <conditional name="call_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	446 <param name="settings" value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	447 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	448 <conditional name="filter_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	449 <param name="settings" value="dream3_settings" />
1 fd901d18b081 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177 iuc parents: 0 diff changeset	450 </conditional>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	451 <output name="output">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	452 <expand macro="test_mentions_contig" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	453 <expand macro="test_mentions_filters" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	454 </output>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	455 </test>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	456 <test expect_num_outputs="1">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	457 <!-- run without post-filters -->
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	458 <conditional name="reference">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	459 <param name="source" value="history" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	460 <param name="genome" value="hg19_chrM.fa" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	461 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	462 <param name="normal_bam" value="control_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	463 <param name="tumor_bam" value="tumor_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	464 <param name="split_output" value="false" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	465 <conditional name="call_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	466 <param name="settings" value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	467 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	468 <conditional name="filter_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	469 <param name="settings" value="no_filter" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	470 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	471 <output name="output">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	472 <expand macro="test_mentions_contig" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	473 <expand macro="test_not_mentions_filters" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	474 </output>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	475 </test>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	476 <test expect_num_outputs="1">
7 2ea345eef4e2 "planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit fcf5ac14629c694f0f64773fab0428b1e78fe156" iuc parents: 6 diff changeset	477 <!-- run with custom post-filters -->
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	478 <conditional name="reference">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	479 <param name="source" value="history" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	480 <param name="genome" value="hg19_chrM.fa" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	481 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	482 <param name="normal_bam" value="control_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	483 <param name="tumor_bam" value="tumor_chrM.bam" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	484 <param name="split_output" value="false" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	485 <conditional name="call_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	486 <param name="settings" value="varscan_defaults" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	487 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	488 <conditional name="filter_params">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	489 <param name="settings" value="custom" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	490 <param name="min_ref_basequal" value="28" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	491 <param name="min_var_basequal" value="28" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	492 </conditional>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	493 <output name="output">
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	494 <expand macro="test_mentions_contig" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	495 <expand macro="test_mentions_filters" />
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	496 </output>
1 fd901d18b081 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177 iuc parents: 0 diff changeset	497 </test>
6 def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	498 <test expect_num_outputs="1">
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	499 <!-- Test with an input bam with extremely high coverage at a
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	500 variant site (high enough to trigger an AssertionError from
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	501 pysam.libcalignedsegment.get_query_sequences) to see if the
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	502 tool can handle this.
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	503 Also test that the tool doesn't report SNVs against Ns in
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	504 the reference genome (this would lead to more than one variant
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	505 getting called). -->
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	506 <conditional name="reference">
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	507 <param name="source" value="history" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	508 <param name="genome" value="hg19_chrM.fa" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	509 </conditional>
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	510 <param name="normal_bam" value="high_cov_chrM.bam" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	511 <param name="tumor_bam" value="high_cov_chrM.bam" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	512 <param name="split_output" value="false" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	513 <conditional name="call_params">
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	514 <param name="settings" value="varscan_defaults" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	515 </conditional>
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	516 <conditional name="filter_params">
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	517 <param name="settings" value="varscan_defaults" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	518 </conditional>
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	519 <output name="output">
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	520 <expand macro="test_mentions_contig" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	521 <expand macro="test_mentions_filters" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	522 <metadata name="data_lines" value="1" />
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	523 </output>
def508f3149e planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b iuc parents: 4 diff changeset	524 </test>
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	525 </tests>
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	526
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	527 <help>
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	528 @HELP_HEADER@
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	529
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	530 The Varscan Somatic tool for Galaxy
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	531
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	532 This tool wraps the functionality of the ``varscan somatic`` and the
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	533 ``varscan fpfilter`` command line tools.
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	534
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	535 The tool is designed to detect genetic variants in a pair of samples
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	536 representing normal and tumor tissue from the same individual. It classifies
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	537 the variants, according to their most likely origin, as somatic (variant is
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	538 found in the tumor, but not in the normal sample, i.e., is the consequence of
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	539 a somatic mutation event), germline (variant is found in both samples =>
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	540 germline mutation event) and LOH (variant is found in both samples, but
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	541 only the tumor sample appears to be homozygous for it => loss of heterozygosity
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	542 event).
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	543 This classification is encoded in the variant ``INFO`` fields of the VCF output
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	544 produced by the tool in the form of a status code ``SS`` (somatic status),
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	545 where:
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	546
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	547 - ``SS=1`` signifies a likely germline variant,
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	548 - ``SS=2`` a somatic variant
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	549 - ``SS=3`` a LOH variant
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	550
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	551 In addition, ``SS=0`` indicates a possible variant, but with insufficient
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	552 evidence for an, at least, heterozygous state in either individual sample, and
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	553 ``SS=5`` is used for variants of unexplained origin (e.g., variants found in
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	554 the normal, but not in the tumor tissue sample).
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	555
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	556 In a second step, following variant calling, the tool can try to detect likely
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	557 false-positive calls by re-inspecting the data at the variant sites more
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	558 carefully and looking for signs that may indicate problems with the
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	559 sequencing data or its mapping. If a called variant is deemed a possible
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	560 false-positive at this step, this gets indicated in the ``FILTER`` field of the
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	561 variant record in the VCF output. For high confidence variants passing all
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	562 posterior (applied after variant calling) filters the value of the field will
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	563 be ``PASS``, for variants failing any of the posterior filters the value will
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	564 be a ``;``-separated list of the problematic filters.
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	565
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	566
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	567 Input
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	568
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	569 The tool takes as input a reference genome (in fasta format) and a pair of
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	570 aligned reads datasets (bam format).
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	571
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	572 Output
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	573
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	574 A VCF dataset of called variants. When asked to *Generate separate output
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	575 datasets for SNP and indel calls*, the tool will behave like the
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	576 ``varscan somatic`` command line tool and produce two VCF datasets - one with
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	577 just the single nucleotide variants, while the other one will store
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	578 insertion/deletion variants.
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	579
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	580 Options
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	581
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	582 Estimated purity of normal sample / of tumor sample
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	583
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	584 Since, in practice, it is often impossible to isolate tissue samples without
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	585 contamination from surrounding tissue or from invading cells, these two fields
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	586 let you indicate your estimate of the purity of the two samples (as fractions
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	587 between 0 and 1, where 1 would indicate a contamination-free sample and 0.5 a
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	588 sample to which the desired tissue contributes only 50%, while the other 50%
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	589 consist of cells from the other tissue type).
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	590
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	591 Settings for Variant Calling
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	592
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	593 Settings in this section will affect the steps of variant calling and
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	594 classification. You can accept VarScan's default values for the corresponding
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	595 parameters or customize them according to your needs.
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	596
2 d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	597 Settings for Posterior Variant Filtering
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	598
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	599 Use the parameters in this section to configure the false-positive filtering
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	600 step that follows variant calling and classification. These settings will not
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	601 influence the number of variants detected nor their classification, but may
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	602 change the ``FILTER`` field of variant records to indicate which variants
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	603 failed to pass certain filters. You can use this information with downstream
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	604 tools to exclude certain variants from further analysis steps or include only
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	605 high confidence variants that passed all filters (those with ``PASS`` as their
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	606 ``INFO`` field value. You can accept the orignal filter defaults of the
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	607 ``varscan fpfilter`` command line tool, use the settings established for the
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	608 tool in the `DREAM3 challenge`_, or choose to customize the settings.
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	609 Alternatively, you can also choose to skip posterior filtering entirely, in
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	610 which case all variants will have their ``INFO`` field set to ``PASS``.
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	611
d0960ef07e55 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3932667bb4f6770a671141f7aab1f326e6dd1919 iuc parents: 1 diff changeset	612 .. _DREAM3 challenge: https://www.synapse.org/#!Synapse:syn312572/wiki/58893
0 6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	613 </help>
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	614 <expand macro="citations" />
6360e01685e1 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 44c3f913e091bfdb94870ec3181390ad98711797 iuc parents: diff changeset	615 </tool>

Mercurial > repos > iuc > varscan_somatic

annotate varscan_somatic.xml @ 7:2ea345eef4e2 draft