trtools: DumpSTR/dumpSTR.xml annotate

annotate DumpSTR/dumpSTR.xml @ 1:8e8cf43f6836 draft default tip

planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390

author	michal_klinka
date	Sun, 15 May 2022 15:23:59 +0000
parents	ecf8c4f9f8ba
children

rev	line source
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	1 <tool id="dumpSTR" name="DumpSTR" version="@tool_version@">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	2 <description>DumpSTR filters VCF files with TR genotypes, performing call-level and locus-level filtering, and
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	3 outputs a filtered VCF file.
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	4 </description>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	5
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	6 <macros>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	7 <import>macros.xml</import>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	8 </macros>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	9
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	10 <expand macro="requirements"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	11 <version_command>dumpSTR --version</version_command>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	12 <command detect_errors="exit_code"><![CDATA[dumpSTR
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	13 ## h definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	14 #if $options.h:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	15 -h
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	16 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	17 ## end h definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	18 ## vcf definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	19 #if $input_output.vcf:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	20 --vcf $input_output.vcf
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	21 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	22 ## end vcf definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	23 ## out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	24 #if $input_output.out:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	25 --out $input_output.out
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	26 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	27 ## end out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	28 ## zip definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	29 #if $input_output.zip:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	30 --zip
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	31 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	32 ## end zip definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	33 ## vcftype definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	34 #if $input_output.vcftype:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	35 --vcftype $input_output.vcftype
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	36 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	37 ## end vcftype definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	38 ## min_locus_callrate definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	39 #if $locus_level_filters__tool_agnostic_.min_locus_callrate:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	40 --min-locus-callrate $locus_level_filters__tool_agnostic_.min_locus_callrate
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	41 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	42 ## end min_locus_callrate definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	43 ## min_locus_hwep definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	44 #if $locus_level_filters__tool_agnostic_.min_locus_hwep:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	45 --min-locus-hwep $locus_level_filters__tool_agnostic_.min_locus_hwep
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	46 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	47 ## end min_locus_hwep definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	48 ## min_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	49 #if $locus_level_filters__tool_agnostic_.min_locus_het:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	50 --min-locus-het $locus_level_filters__tool_agnostic_.min_locus_het
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	51 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	52 ## end min_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	53 ## max_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	54 #if $locus_level_filters__tool_agnostic_.max_locus_het:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	55 --max-locus-het $locus_level_filters__tool_agnostic_.max_locus_het
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	56 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	57 ## end max_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	58 ## use_length definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	59 #if $locus_level_filters__tool_agnostic_.use_length:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	60 --use-length
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	61 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	62 ## end use_length definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	63 ## filter_regions definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	64 #if $locus_level_filters__tool_agnostic_.filter_regions:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	65 --filter-regions $locus_level_filters__tool_agnostic_.filter_regions
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	66 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	67 ## end filter_regions definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	68 ## filter_regions_names definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	69 #if $locus_level_filters__tool_agnostic_.filter_regions_names:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	70 --filter-regions-names $locus_level_filters__tool_agnostic_.filter_regions_names
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	71 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	72 ## end filter_regions_names definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	73 ## filter_hrun definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	74 #if $locus_level_filters__tool_agnostic_.filter_hrun:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	75 --filter-hrun
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	76 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	77 ## end filter_hrun definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	78 ## drop_filtered definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	79 #if $locus_level_filters__tool_agnostic_.drop_filtered:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	80 --drop-filtered
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	81 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	82 ## end drop_filtered definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	83 ## hipstr_max_call_flank_indel definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	84 #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	85 --hipstr-max-call-flank-indel $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	86 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	87 ## end hipstr_max_call_flank_indel definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	88 ## hipstr_max_call_stutter definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	89 #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	90 --hipstr-max-call-stutter $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	91 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	92 ## end hipstr_max_call_stutter definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	93 ## hipstr_min_supp_reads definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	94 #if $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	95 --hipstr-min-supp-reads $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	96 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	97 ## end hipstr_min_supp_reads definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	98 ## hipstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	99 #if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	100 --hipstr-min-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	101 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	102 ## end hipstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	103 ## hipstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	104 #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	105 --hipstr-max-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	106 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	107 ## end hipstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	108 ## hipstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	109 #if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	110 --hipstr-min-call-Q $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	111 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	112 ## end hipstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	113 ## gangstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	114 #if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	115 --gangstr-min-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	116 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	117 ## end gangstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	118 ## gangstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	119 #if $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	120 --gangstr-max-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	121 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	122 ## end gangstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	123 ## gangstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	124 #if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	125 --gangstr-min-call-Q $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	126 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	127 ## end gangstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	128 ## gangstr_expansion_prob_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	129 #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	130 --gangstr-expansion-prob-het $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	131 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	132 ## end gangstr_expansion_prob_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	133 ## gangstr_expansion_prob_hom definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	134 #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	135 --gangstr-expansion-prob-hom $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	136 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	137 ## end gangstr_expansion_prob_hom definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	138 ## gangstr_expansion_prob_total definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	139 #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	140 --gangstr-expansion-prob-total $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	141 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	142 ## end gangstr_expansion_prob_total definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	143 ## gangstr_filter_span_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	144 #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_span_only:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	145 --gangstr-filter-span-only
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	146 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	147 ## end gangstr_filter_span_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	148 ## gangstr_filter_spanbound_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	149 #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_spanbound_only:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	150 --gangstr-filter-spanbound-only
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	151 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	152 ## end gangstr_filter_spanbound_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	153 ## gangstr_filter_badCI definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	154 #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_badCI:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	155 --gangstr-filter-badCI
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	156 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	157 ## end gangstr_filter_badCI definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	158 ## gangstr_readlen definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	159 #if $call_level_filters_specific_to_gangstr_output.gangstr_readlen:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	160 --gangstr-readlen $call_level_filters_specific_to_gangstr_output.gangstr_readlen
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	161 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	162 ## end gangstr_readlen definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	163 ## advntr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	164 #if $call_level_filters_specific_to_advntr_output.advntr_min_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	165 --advntr-min-call-DP $call_level_filters_specific_to_advntr_output.advntr_min_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	166 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	167 ## end advntr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	168 ## advntr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	169 #if $call_level_filters_specific_to_advntr_output.advntr_max_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	170 --advntr-max-call-DP $call_level_filters_specific_to_advntr_output.advntr_max_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	171 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	172 ## end advntr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	173 ## advntr_min_spanning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	174 #if $call_level_filters_specific_to_advntr_output.advntr_min_spanning:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	175 --advntr-min-spanning $call_level_filters_specific_to_advntr_output.advntr_min_spanning
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	176 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	177 ## end advntr_min_spanning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	178 ## advntr_min_flanking definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	179 #if $call_level_filters_specific_to_advntr_output.advntr_min_flanking:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	180 --advntr-min-flanking $call_level_filters_specific_to_advntr_output.advntr_min_flanking
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	181 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	182 ## end advntr_min_flanking definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	183 ## advntr_min_ML definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	184 #if $call_level_filters_specific_to_advntr_output.advntr_min_ML:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	185 --advntr-min-ML $call_level_filters_specific_to_advntr_output.advntr_min_ML
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	186 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	187 ## end advntr_min_ML definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	188 ## eh_min_ADFL definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	189 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	190 --eh-min-ADFL $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	191 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	192 ## end eh_min_ADFL definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	193 ## eh_min_ADIR definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	194 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	195 --eh-min-ADIR $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	196 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	197 ## end eh_min_ADIR definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	198 ## eh_min_ADSP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	199 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	200 --eh-min-ADSP $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	201 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	202 ## end eh_min_ADSP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	203 ## eh_min_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	204 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	205 --eh-min-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	206 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	207 ## end eh_min_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	208 ## eh_max_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	209 #if $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	210 --eh-max-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	211 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	212 ## end eh_max_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	213 ## popstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	214 #if $call_level_filters_specific_to_popstr_output.popstr_min_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	215 --popstr-min-call-DP $call_level_filters_specific_to_popstr_output.popstr_min_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	216 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	217 ## end popstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	218 ## popstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	219 #if $call_level_filters_specific_to_popstr_output.popstr_max_call_DP:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	220 --popstr-max-call-DP $call_level_filters_specific_to_popstr_output.popstr_max_call_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	221 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	222 ## end popstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	223 ## popstr_require_support definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	224 #if $call_level_filters_specific_to_popstr_output.popstr_require_support:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	225 --popstr-require-support $call_level_filters_specific_to_popstr_output.popstr_require_support
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	226 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	227 ## end popstr_require_support definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	228 ## num_records definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	229 #if $debugging_parameters.num_records:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	230 --num-records $debugging_parameters.num_records
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	231 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	232 ## end num_records definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	233 ## die_on_warning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	234 #if $debugging_parameters.die_on_warning:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	235 --die-on-warning
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	236 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	237 ## end die_on_warning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	238 ## verbose definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	239 #if $debugging_parameters.verbose:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	240 --verbose
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	241 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	242 ## end verbose definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	243 ## version definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	244 #if $version313f.version:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	245 --version
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	246 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	247 ## end version definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	248 1>$stdout 2>$stderr
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	249 ]]></command>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	250
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	251
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	252 <inputs>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	253
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	254
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	255 <section name="options" title="options" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	256 <param argument="-h" type="boolean" optional="true" label="help" help="show this help message and exit"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	257 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	258 <section name="input_output" title="Input/output" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	259 <param argument="--vcf" type="data" format="vcf" optional="false" label="vcf" help="Input STR VCF file"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	260 <param argument="--out" type="text" optional="false" label="out" help="Prefix for output files"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	261 <param argument="--zip" type="boolean" optional="true" label="zip"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	262 help="Produce a bgzipped and tabix indexed output VCF"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	263 <param argument="--vcftype" type="select" optional="true" label="vcftype"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	264 help="Genotyper that was used to create this VCF input">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	265 <expand macro="vcfTypes"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	266 </param>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	267 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	268 <section name="locus_level_filters__tool_agnostic_" title="Locus-level filters (tool agnostic)"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	269 expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	270 <param argument="--min-locus-callrate" type="float" optional="true" label="min_locus_callrate"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	271 help="Minimum locus call rate"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	272 <param argument="--min-locus-hwep" type="float" optional="true" label="min_locus_hwep"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	273 help="Filter loci failing HWE at this p-value threshold"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	274 <param argument="--min-locus-het" type="float" optional="true" label="min_locus_het"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	275 help="Minimum locus heterozygosity"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	276 <param argument="--max-locus-het" type="float" optional="true" label="max_locus_het"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	277 help="Maximum locus heterozygosity"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	278 <param argument="--use-length" type="boolean" optional="true" label="use_length"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	279 help="Calculate per-locus stats (het, HWE) collapsing alleles by length"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	280 <param argument="--filter-regions" type="text" optional="true" label="filter_regions"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	281 help="Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	282 <param argument="--filter-regions-names" type="text" optional="true" label="filter_regions_names"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	283 help="Comma-separated list of filter names for each BED filter file"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	284 <param argument="--filter-hrun" type="boolean" optional="true" label="filter_hrun"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	285 help="Filter STRs with long homopolymer runs."/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	286 <param argument="--drop-filtered" type="boolean" optional="true" label="drop_filtered"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	287 help="Drop filtered records from output"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	288 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	289 <section name="call_level_filters_specific_to_hipstr_output"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	290 title="Call-level filters specific to HipSTR output" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	291 <param argument="--hipstr-max-call-flank-indel" type="float" optional="true"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	292 label="hipstr_max_call_flank_indel" help="Maximum call flank indel rate"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	293 <param argument="--hipstr-max-call-stutter" type="float" optional="true" label="hipstr_max_call_stutter"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	294 help="Maximum call stutter rate"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	295 <param argument="--hipstr-min-supp-reads" type="integer" optional="true" label="hipstr_min_supp_reads"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	296 help="Minimum supporting reads for each allele"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	297 <param argument="--hipstr-min-call-DP" type="integer" optional="true" label="hipstr_min_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	298 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	299 <param argument="--hipstr-max-call-DP" type="integer" optional="true" label="hipstr_max_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	300 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	301 <param argument="--hipstr-min-call-Q" type="float" optional="true" label="hipstr_min_call_Q"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	302 help="Minimum call quality score"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	303 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	304 <section name="call_level_filters_specific_to_gangstr_output"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	305 title="Call-level filters specific to GangSTR output" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	306 <param argument="--gangstr-min-call-DP" type="integer" optional="true" label="gangstr_min_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	307 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	308 <param argument="--gangstr-max-call-DP" type="integer" optional="true" label="gangstr_max_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	309 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	310 <param argument="--gangstr-min-call-Q" type="float" optional="true" label="gangstr_min_call_Q"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	311 help="Minimum call quality score"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	312 <param argument="--gangstr-expansion-prob-het" type="float" optional="true"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	313 label="gangstr_expansion_prob_het"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	314 help="Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less than this"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	315 <param argument="--gangstr-expansion-prob-hom" type="float" optional="true"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	316 label="gangstr_expansion_prob_hom"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	317 help="Expansion prob-value threshold. Filters calls with probability of homozygous expansion less than this"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	318 <param argument="--gangstr-expansion-prob-total" type="float" optional="true"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	319 label="gangstr_expansion_prob_total"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	320 help="Expansion prob-value threshold. Filters calls with probability of total expansion less than this"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	321 <param argument="--gangstr-filter-span-only" type="boolean" optional="true" label="gangstr_filter_span_only"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	322 help="Filter out all calls that only have spanning read support"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	323 <param argument="--gangstr-filter-spanbound-only" type="boolean" optional="true"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	324 label="gangstr_filter_spanbound_only" help="Filter out all reads except spanning and bounding"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	325 <param argument="--gangstr-filter-badCI" type="boolean" optional="true" label="gangstr_filter_badCI"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	326 help="Filter regions where the ML estimate is not in the CI"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	327 <param argument="--gangstr-readlen" type="integer" optional="true" label="gangstr_readlen"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	328 help="Read length used (bp). Required if using --require-support"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	329 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	330 <section name="call_level_filters_specific_to_advntr_output"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	331 title="Call-level filters specific to adVNTR output" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	332 <param argument="--advntr-min-call-DP" type="integer" optional="true" label="advntr_min_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	333 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	334 <param argument="--advntr-max-call-DP" type="integer" optional="true" label="advntr_max_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	335 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	336 <param argument="--advntr-min-spanning" type="integer" optional="true" label="advntr_min_spanning"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	337 help="Minimum spanning read count (SR field)"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	338 <param argument="--advntr-min-flanking" type="integer" optional="true" label="advntr_min_flanking"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	339 help="Minimum flanking read count (FR field)"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	340 <param argument="--advntr-min-ML" type="float" optional="true" label="advntr_min_ML"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	341 help="Minimum value of maximum likelihood (ML field)"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	342 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	343 <section name="call_level_filters_specific_to_expansionhunter_output"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	344 title="Call-level filters specific to ExpansionHunter output" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	345 <param argument="--eh-min-ADFL" type="integer" optional="true" label="eh_min_ADFL"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	346 help="Minimum number of flanking reads consistent with the allele"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	347 <param argument="--eh-min-ADIR" type="integer" optional="true" label="eh_min_ADIR"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	348 help="Minimum number of in-repeat reads consistent with the allele"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	349 <param argument="--eh-min-ADSP" type="integer" optional="true" label="eh_min_ADSP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	350 help="Minimum number of spanning reads consistent with the allele"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	351 <param argument="--eh-min-call-LC" type="integer" optional="true" label="eh_min_call_LC"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	352 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	353 <param argument="--eh-max-call-LC" type="integer" optional="true" label="eh_max_call_LC"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	354 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	355 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	356 <section name="call_level_filters_specific_to_popstr_output"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	357 title="Call-level filters specific to PopSTR output" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	358 <param argument="--popstr-min-call-DP" type="integer" optional="true" label="popstr_min_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	359 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	360 <param argument="--popstr-max-call-DP" type="integer" optional="true" label="popstr_max_call_DP"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	361 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	362 <param argument="--popstr-require-support" type="integer" optional="true" label="popstr_require_support"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	363 help="Require each allele call to have at least n supporting reads"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	364 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	365 <section name="debugging_parameters" title="Debugging parameters" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	366 <param argument="--num-records" type="integer" optional="true" label="num_records"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	367 help="Only process this many records"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	368 <param argument="--die-on-warning" type="boolean" optional="true" label="die_on_warning"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	369 help="Quit if a record can't be parsed"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	370 <param argument="--verbose" type="boolean" optional="true" label="verbose" help="Print out extra info"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	371 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	372 <section name="version313f" title="Version" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	373 <param argument="--version" type="boolean" optional="true" label="version"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	374 help="show program's version number and exit"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	375 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	376 </inputs>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	377
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	378
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	379 <outputs>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	380 <data name="stdout" label="STDOUT output" format="txt"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	381
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	382 <data name="main_output" label="Main output">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	383 <discover_datasets format="vcf" pattern="(?P<designation>.+)\.vcf" visible="true"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	384 assign_primary_output="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	385 <discover_datasets format="tabular" pattern="(?P<designation>.+)\.tab" visible="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	386 </data>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	387
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	388 <data name="stderr" label="STDERR output" format="txt">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	389 <discover_datasets format="vcf_bgzip" pattern="(?P<designation>.+)\.vcf.gz" visible="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	390 <discover_datasets format="tabix" pattern="(?P<designation>.+)\.vcf.gz.tbi" visible="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	391 </data>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	392
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	393 </outputs>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	394
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	395
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	396 <tests>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	397 <test>
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	398 <section name="input_output">
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	399 <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	400 <param name="out" value="test_result"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	401 <param name="vcftype" value="hipstr"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	402 <param name="zip" value="false"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	403 </section>
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	404 <section name="locus_level_filters__tool_agnostic_">
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	405 <param name="min_locus_callrate" value="0.1"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	406 <param name="use_length" value="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	407 <param name="drop_filtered" value="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	408 </section>
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	409 <section name="call_level_filters_specific_to_hipstr_output">
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	410 <param name="hipstr_max_call_flank_indel" value="0.2"/>
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	411 <param name="hipstr_min_call_Q" value="0.4"/>
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	412 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	413
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	414 <output name="stdout" file="stdout.txt"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	415
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	416 <output name="main_output">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	417 <discovered_dataset designation="test_result.loclog" file="test_result.loclog.tab"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	418 <discovered_dataset designation="test_result.samplog" file="test_result.samplog.tab"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	419 <discovered_dataset designation="test_result">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	420 <assert_contents>
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	421 <has_size value="4062163" delta="1000"/>
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	422 <has_text text="##fileformat=VCFv4.1"/>
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	423 <has_n_lines n="9047" delta="1"/>
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	424 </assert_contents>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	425 </discovered_dataset>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	426 </output>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	427 <output name="stderr" file="stderr.txt"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	428
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	429 </test>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	430 </tests>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	431
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	432
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	433 <help>usage: pygalgen [-h] --vcf VCF --out OUT [--zip] [--vcftype VCFTYPE] [--min-locus-callrate MIN_LOCUS_CALLRATE]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	434 [--min-locus-hwep MIN_LOCUS_HWEP] [--min-locus-het MIN_LOCUS_HET] [--max-locus-het MAX_LOCUS_HET]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	435 [--use-length] [--filter-regions FILTER_REGIONS] [--filter-regions-names FILTER_REGIONS_NAMES]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	436 [--filter-hrun] [--drop-filtered] [--hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	437 [--hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER] [--hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	438 [--hipstr-min-call-DP HIPSTR_MIN_CALL_DP] [--hipstr-max-call-DP HIPSTR_MAX_CALL_DP]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	439 [--hipstr-min-call-Q HIPSTR_MIN_CALL_Q] [--gangstr-min-call-DP GANGSTR_MIN_CALL_DP]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	440 [--gangstr-max-call-DP GANGSTR_MAX_CALL_DP] [--gangstr-min-call-Q GANGSTR_MIN_CALL_Q]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	441 [--gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	442 [--gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	443 [--gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL] [--gangstr-filter-span-only]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	444 [--gangstr-filter-spanbound-only] [--gangstr-filter-badCI] [--gangstr-readlen GANGSTR_READLEN]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	445 [--advntr-min-call-DP ADVNTR_MIN_CALL_DP] [--advntr-max-call-DP ADVNTR_MAX_CALL_DP]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	446 [--advntr-min-spanning ADVNTR_MIN_SPANNING] [--advntr-min-flanking ADVNTR_MIN_FLANKING]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	447 [--advntr-min-ML ADVNTR_MIN_ML] [--eh-min-ADFL EH_MIN_ADFL] [--eh-min-ADIR EH_MIN_ADIR]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	448 [--eh-min-ADSP EH_MIN_ADSP] [--eh-min-call-LC EH_MIN_CALL_LC] [--eh-max-call-LC EH_MAX_CALL_LC]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	449 [--popstr-min-call-DP POPSTR_MIN_CALL_DP] [--popstr-max-call-DP POPSTR_MAX_CALL_DP]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	450 [--popstr-require-support POPSTR_REQUIRE_SUPPORT] [--num-records NUM_RECORDS] [--die-on-warning]
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	451 [--verbose] [--version]
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	452
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	453 options:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	454 -h, --help show this help message and exit
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	455
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	456 Input/output:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	457 --vcf VCF Input STR VCF file
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	458 --out OUT Prefix for output files
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	459 --zip Produce a bgzipped and tabix indexed output VCF
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	460 --vcftype VCFTYPE Name of the genotyper that generated the input VCF
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	461
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	462 Locus-level filters (tool agnostic):
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	463 --min-locus-callrate MIN_LOCUS_CALLRATE
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	464 Minimum locus call rate
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	465 --min-locus-hwep MIN_LOCUS_HWEP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	466 Filter loci failing HWE at this p-value threshold
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	467 --min-locus-het MIN_LOCUS_HET
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	468 Minimum locus heterozygosity
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	469 --max-locus-het MAX_LOCUS_HET
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	470 Maximum locus heterozygosity
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	471 --use-length Calculate per-locus stats (het, HWE) collapsing alleles by length
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	472 --filter-regions FILTER_REGIONS
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	473 Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	474 --filter-regions-names FILTER_REGIONS_NAMES
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	475 Comma-separated list of filter names for each BED filter file
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	476 --filter-hrun Filter STRs with long homopolymer runs.
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	477 --drop-filtered Drop filtered records from output
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	478
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	479 Call-level filters specific to HipSTR output:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	480 --hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	481 Maximum call flank indel rate
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	482 --hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	483 Maximum call stutter rate
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	484 --hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	485 Minimum supporting reads for each allele
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	486 --hipstr-min-call-DP HIPSTR_MIN_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	487 Minimum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	488 --hipstr-max-call-DP HIPSTR_MAX_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	489 Maximum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	490 --hipstr-min-call-Q HIPSTR_MIN_CALL_Q
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	491 Minimum call quality score
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	492
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	493 Call-level filters specific to GangSTR output:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	494 --gangstr-min-call-DP GANGSTR_MIN_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	495 Minimum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	496 --gangstr-max-call-DP GANGSTR_MAX_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	497 Maximum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	498 --gangstr-min-call-Q GANGSTR_MIN_CALL_Q
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	499 Minimum call quality score
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	500 --gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	501 Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	502 than this
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	503 --gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	504 Expansion prob-value threshold. Filters calls with probability of homozygous expansion less
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	505 than this
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	506 --gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	507 Expansion prob-value threshold. Filters calls with probability of total expansion less than
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	508 this
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	509 --gangstr-filter-span-only
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	510 Filter out all calls that only have spanning read support
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	511 --gangstr-filter-spanbound-only
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	512 Filter out all reads except spanning and bounding
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	513 --gangstr-filter-badCI
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	514 Filter regions where the ML estimate is not in the CI
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	515 --gangstr-readlen GANGSTR_READLEN
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	516 Read length used (bp). Required if using --require-support
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	517
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	518 Call-level filters specific to adVNTR output:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	519 --advntr-min-call-DP ADVNTR_MIN_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	520 Minimum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	521 --advntr-max-call-DP ADVNTR_MAX_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	522 Maximum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	523 --advntr-min-spanning ADVNTR_MIN_SPANNING
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	524 Minimum spanning read count (SR field)
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	525 --advntr-min-flanking ADVNTR_MIN_FLANKING
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	526 Minimum flanking read count (FR field)
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	527 --advntr-min-ML ADVNTR_MIN_ML
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	528 Minimum value of maximum likelihood (ML field)
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	529
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	530 Call-level filters specific to ExpansionHunter output:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	531 --eh-min-ADFL EH_MIN_ADFL
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	532 Minimum number of flanking reads consistent with the allele
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	533 --eh-min-ADIR EH_MIN_ADIR
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	534 Minimum number of in-repeat reads consistent with the allele
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	535 --eh-min-ADSP EH_MIN_ADSP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	536 Minimum number of spanning reads consistent with the allele
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	537 --eh-min-call-LC EH_MIN_CALL_LC
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	538 Minimum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	539 --eh-max-call-LC EH_MAX_CALL_LC
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	540 Maximum call coverage
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	541
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	542 Call-level filters specific to PopSTR output:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	543 --popstr-min-call-DP POPSTR_MIN_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	544 Minimum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	545 --popstr-max-call-DP POPSTR_MAX_CALL_DP
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	546 Maximum call coverage
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	547 --popstr-require-support POPSTR_REQUIRE_SUPPORT
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	548 Require each allele call to have at least n supporting reads
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	549
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	550 Debugging parameters:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	551 --num-records NUM_RECORDS
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	552 Only process this many records
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	553 --die-on-warning Quit if a record can't be parsed
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	554 --verbose Print out extra info
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	555
1 8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	556 Version:
8e8cf43f6836 planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390 michal_klinka parents: 0 diff changeset	557 --version show program's version number and exit
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	558 </help>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	559
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	560
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	561 <citations>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	562 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	563 author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	564 year = {2020},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	565 title = {TRTools},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	566 publisher = {GitHub},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	567 journal = {GitHub repository},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	568 url = {https://github.com/gymreklab/trtools},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	569 }
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	570 </citation>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	571 </citations>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	572 </tool>

Mercurial > repos > michal_klinka > trtools

annotate DumpSTR/dumpSTR.xml @ 1:8e8cf43f6836 draft default tip