trtools: DumpSTR/dumpSTR.xml annotate

annotate DumpSTR/dumpSTR.xml @ 0:ecf8c4f9f8ba draft

"planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"

author	michal_klinka
date	Sat, 23 Apr 2022 16:34:03 +0000
parents
children	8e8cf43f6836

rev	line source
0 ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	1 <?xml version="1.0" ?>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	2 <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	3 <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	4 outputs a filtered VCF file.
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	5 </description>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	6
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	7 <macros>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	8 <import>macros.xml</import>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	9 </macros>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	10
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	11 <expand macro="requirements"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	12 <version_command>dumpSTR --version</version_command>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[dumpSTR
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	14 ## h definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	15 #if $options.h:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	16 -h
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	17 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	18 ## end h definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	19 ## vcf definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	20 #if $input_output.vcf:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	21 --vcf $input_output.vcf
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	22 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	23 ## end vcf definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	24 ## out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	25 #if $input_output.out:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	26 --out $input_output.out
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	27 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	28 ## end out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	29 ## zip definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	30 #if $input_output.zip:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	31 --zip
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	32 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	33 ## end zip definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	34 ## vcftype definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	35 #if $input_output.vcftype:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	36 --vcftype $input_output.vcftype
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	37 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	38 ## end vcftype definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	39 ## min_locus_callrate definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	40 #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	41 --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	42 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	43 ## end min_locus_callrate definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	44 ## min_locus_hwep definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	45 #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	46 --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	47 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	48 ## end min_locus_hwep definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	49 ## min_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	50 #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	51 --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	52 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	53 ## end min_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	54 ## max_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	55 #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	56 --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	57 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	58 ## end max_locus_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	59 ## use_length definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	60 #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	61 --use-length
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	62 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	63 ## end use_length definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	64 ## filter_regions definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	65 #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	66 --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	67 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	68 ## end filter_regions definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	69 ## filter_regions_names definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	70 #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	71 --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	72 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	73 ## end filter_regions_names definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	74 ## filter_hrun definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	75 #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	76 --filter-hrun
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	77 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	78 ## end filter_hrun definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	79 ## drop_filtered definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	80 #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	81 --drop-filtered
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	82 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	83 ## end drop_filtered definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	84 ## hipstr_max_call_flank_indel definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	85 #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	86 --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	87 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	88 ## end hipstr_max_call_flank_indel definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	89 ## hipstr_max_call_stutter definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	90 #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	91 --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	92 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	93 ## end hipstr_max_call_stutter definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	94 ## hipstr_min_supp_reads definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	95 #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	96 --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	97 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	98 ## end hipstr_min_supp_reads definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	99 ## hipstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	100 #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	101 --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	102 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	103 ## end hipstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	104 ## hipstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	105 #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	106 --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	107 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	108 ## end hipstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	109 ## hipstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	110 #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	111 --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	112 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	113 ## end hipstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	114 ## gangstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	115 #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	116 --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	117 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	118 ## end gangstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	119 ## gangstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	120 #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	121 --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	122 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	123 ## end gangstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	124 ## gangstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	125 #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	126 --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	127 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	128 ## end gangstr_min_call_Q definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	129 ## gangstr_expansion_prob_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	130 #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	131 --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	132 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	133 ## end gangstr_expansion_prob_het definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	134 ## gangstr_expansion_prob_hom definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	135 #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	136 --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	137 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	138 ## end gangstr_expansion_prob_hom definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	139 ## gangstr_expansion_prob_total definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	140 #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	141 --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	142 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	143 ## end gangstr_expansion_prob_total definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	144 ## gangstr_filter_span_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	145 #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	146 --gangstr-filter-span-only
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	147 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	148 ## end gangstr_filter_span_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	149 ## gangstr_filter_spanbound_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	150 #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	151 --gangstr-filter-spanbound-only
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	152 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	153 ## end gangstr_filter_spanbound_only definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	154 ## gangstr_filter_badCI definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	155 #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	156 --gangstr-filter-badCI
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	157 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	158 ## end gangstr_filter_badCI definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	159 ## gangstr_readlen definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	160 #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	161 --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	162 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	163 ## end gangstr_readlen definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	164 ## advntr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	165 #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	166 --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	167 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	168 ## end advntr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	169 ## advntr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	170 #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	171 --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	172 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	173 ## end advntr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	174 ## advntr_min_spanning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	175 #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	176 --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	177 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	178 ## end advntr_min_spanning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	179 ## advntr_min_flanking definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	180 #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	181 --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	182 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	183 ## end advntr_min_flanking definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	184 ## advntr_min_ML definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	185 #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	186 --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	187 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	188 ## end advntr_min_ML definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	189 ## eh_min_ADFL definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	190 #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	191 --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	192 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	193 ## end eh_min_ADFL definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	194 ## eh_min_ADIR definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	195 #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	196 --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	197 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	198 ## end eh_min_ADIR definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	199 ## eh_min_ADSP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	200 #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	201 --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	202 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	203 ## end eh_min_ADSP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	204 ## eh_min_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	205 #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	206 --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	207 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	208 ## end eh_min_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	209 ## eh_max_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	210 #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	211 --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	212 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	213 ## end eh_max_call_LC definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	214 ## popstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	215 #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	216 --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	217 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	218 ## end popstr_min_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	219 ## popstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	220 #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	221 --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	222 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	223 ## end popstr_max_call_DP definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	224 ## popstr_require_support definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	225 #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	226 --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	227 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	228 ## end popstr_require_support definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	229 ## num_records definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	230 #if $debugging_parameters.num_records:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	231 --num-records $debugging_parameters.num_records
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	232 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	233 ## end num_records definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	234 ## die_on_warning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	235 #if $debugging_parameters.die_on_warning:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	236 --die-on-warning
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	237 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	238 ## end die_on_warning definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	239 ## verbose definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	240 #if $debugging_parameters.verbose:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	241 --verbose
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	242 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	243 ## end verbose definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	244 ## version definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	245 #if $version313f.version:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	246 --version
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	247 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	248 ## end version definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	249 1>$stdout 2>$stderr
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	250 ]]></command>
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
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	253 <inputs>
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
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	256 <section name="options" title="options" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	257 <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	258 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	259 <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	260 <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	261 <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	262 <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	263 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	264 <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	265 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	266 <expand macro="vcfTypes"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	267 </param>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	268 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	269 <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	270 expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	271 <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	272 help="Minimum locus call rate"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	273 <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	274 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	275 <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	276 help="Minimum locus heterozygosity"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	277 <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	278 help="Maximum locus heterozygosity"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	279 <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	280 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	281 <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	282 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	283 <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	284 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	285 <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	286 help="Filter STRs with long homopolymer runs."/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	287 <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	288 help="Drop filtered records from output"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	289 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	290 <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	291 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	292 <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	293 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	294 <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	295 help="Maximum call stutter rate"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	296 <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	297 help="Minimum supporting reads for each allele"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	298 <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	299 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	300 <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	301 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	302 <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	303 help="Minimum call quality score"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	304 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	305 <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	306 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	307 <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	308 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	309 <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	310 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	311 <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	312 help="Minimum call quality score"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	313 <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	314 label="gangstr_expansion_prob_het"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	315 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	316 <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	317 label="gangstr_expansion_prob_hom"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	318 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	319 <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	320 label="gangstr_expansion_prob_total"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	321 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	322 <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	323 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	324 <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	325 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	326 <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	327 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	328 <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	329 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	330 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	331 <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	332 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	333 <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	334 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	335 <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	336 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	337 <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	338 help="Minimum spanning read count (SR field)"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	339 <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	340 help="Minimum flanking read count (FR field)"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	341 <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	342 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	343 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	344 <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	345 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	346 <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	347 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	348 <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	349 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	350 <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	351 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	352 <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	353 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	354 <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	355 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	356 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	357 <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	358 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	359 <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	360 help="Minimum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	361 <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	362 help="Maximum call coverage"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	363 <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	364 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	365 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	366 <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	367 <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	368 help="Only process this many records"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	369 <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	370 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	371 <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	372 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	373 <section name="version313f" title="Version" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	374 <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	375 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	376 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	377 </inputs>
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
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	380 <outputs>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	381 <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	382
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	383 <data name="main_output" label="Main output">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	384 <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	385 assign_primary_output="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	386 <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	387 </data>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	388
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	389 <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	390 <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	391 <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	392 </data>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	393
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	394 </outputs>
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
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	397 <tests>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	398 <test>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	399 <section name="main_params">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	400 <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	401 <param name="out" value="test_result"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	402 <param name="vcftype" value="hipstr"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	403 <param name="zip" value="false"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	404 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	405 <section name="filter_opt">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	406 <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	407 <param name="use_length" value="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	408 <param name="drop_filtered" value="true"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	409 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	410 <section name="filter_call_level">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	411 <section name="hipstr_filters">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	412 <param name="hipstr_max_call_flank_indel" value="0.2"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	413 <param name="hipstr_min_call_Q" value="0.4"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	414 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	415 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	416
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	417 <output name="stdout" file="stdout.txt"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	418
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	419 <output name="main_output">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	420 <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	421 <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	422 <discovered_dataset designation="test_result">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	423 <assert_contents>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	424 <has_size value="4061730" delta="200"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	425 <has_text text="##fileformat=VCFv4.1"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	426 <has_n_lines n="9046"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	427 </assert_contents>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	428 </discovered_dataset>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	429 </output>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	430 <output name="stderr" file="stderr.txt"/>
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 </test>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	433 </tests>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	434
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	435
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	436 <help>usage: main.py [-h] --vcf VCF --out OUT [--zip] [--vcftype VCFTYPE] [--min-locus-callrate MIN_LOCUS_CALLRATE]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	437 [--min-locus-hwep MIN_LOCUS_HWEP] [--min-locus-het MIN_LOCUS_HET] [--max-locus-het MAX_LOCUS_HET] [--use-length]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	438 [--filter-regions FILTER_REGIONS] [--filter-regions-names FILTER_REGIONS_NAMES] [--filter-hrun]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	439 [--drop-filtered] [--hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	440 [--hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER] [--hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	441 [--hipstr-min-call-DP HIPSTR_MIN_CALL_DP] [--hipstr-max-call-DP HIPSTR_MAX_CALL_DP]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	442 [--hipstr-min-call-Q HIPSTR_MIN_CALL_Q] [--gangstr-min-call-DP GANGSTR_MIN_CALL_DP] [--gangstr-max-call-DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	443 GANGSTR_MAX_CALL_DP] [--gangstr-min-call-Q GANGSTR_MIN_CALL_Q]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	444 [--gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET] [--gangstr-expansion-prob-hom
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	445 GANGSTR_EXPANSION_PROB_HOM] [--gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	446 [--gangstr-filter-span-only]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	447 [--gangstr-filter-spanbound-only] [--gangstr-filter-badCI] [--gangstr-readlen GANGSTR_READLEN]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	448 [--advntr-min-call-DP ADVNTR_MIN_CALL_DP] [--advntr-max-call-DP ADVNTR_MAX_CALL_DP]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	449 [--advntr-min-spanning ADVNTR_MIN_SPANNING] [--advntr-min-flanking ADVNTR_MIN_FLANKING] [--advntr-min-ML
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	450 ADVNTR_MIN_ML] [--eh-min-ADFL EH_MIN_ADFL] [--eh-min-ADIR EH_MIN_ADIR] [--eh-min-ADSP EH_MIN_ADSP]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	451 [--eh-min-call-LC EH_MIN_CALL_LC] [--eh-max-call-LC EH_MAX_CALL_LC] [--popstr-min-call-DP POPSTR_MIN_CALL_DP]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	452 [--popstr-max-call-DP POPSTR_MAX_CALL_DP] [--popstr-require-support POPSTR_REQUIRE_SUPPORT]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	453 [--num-records NUM_RECORDS] [--die-on-warning] [--verbose] [--version]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	454
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	455 options:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	456 -h, --help show this help message and exit
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	457
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	458 Input/output:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	459 --vcf VCF Input STR VCF file
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	460 --out OUT Prefix for output files
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	461 --zip 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	462 --vcftype VCFTYPE ##!!## Name trh could not be loaded
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	463
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	464 Locus-level filters (tool agnostic):
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	465 --min-locus-callrate MIN_LOCUS_CALLRATE
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	466 Minimum locus call rate
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	467 --min-locus-hwep MIN_LOCUS_HWEP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	468 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	469 --min-locus-het MIN_LOCUS_HET
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	470 Minimum locus heterozygosity
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	471 --max-locus-het MAX_LOCUS_HET
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	472 Maximum locus heterozygosity
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	473 --use-length 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	474 --filter-regions FILTER_REGIONS
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	475 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	476 --filter-regions-names FILTER_REGIONS_NAMES
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	477 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	478 --filter-hrun Filter STRs with long homopolymer runs.
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	479 --drop-filtered Drop filtered records from output
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	480
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	481 Call-level filters specific to HipSTR output:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	482 --hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	483 Maximum call flank indel rate
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	484 --hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	485 Maximum call stutter rate
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	486 --hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	487 Minimum supporting reads for each allele
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	488 --hipstr-min-call-DP HIPSTR_MIN_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	489 Minimum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	490 --hipstr-max-call-DP HIPSTR_MAX_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	491 Maximum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	492 --hipstr-min-call-Q HIPSTR_MIN_CALL_Q
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	493 Minimum call quality score
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	494
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	495 Call-level filters specific to GangSTR output:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	496 --gangstr-min-call-DP GANGSTR_MIN_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	497 Minimum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	498 --gangstr-max-call-DP GANGSTR_MAX_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	499 Maximum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	500 --gangstr-min-call-Q GANGSTR_MIN_CALL_Q
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	501 Minimum call quality score
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	502 --gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	503 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	504 --gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	505 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	506 --gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	507 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	508 --gangstr-filter-span-only
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	509 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	510 --gangstr-filter-spanbound-only
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	511 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	512 --gangstr-filter-badCI
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	513 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	514 --gangstr-readlen GANGSTR_READLEN
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	515 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	516
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	517 Call-level filters specific to adVNTR output:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	518 --advntr-min-call-DP ADVNTR_MIN_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	519 Minimum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	520 --advntr-max-call-DP ADVNTR_MAX_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	521 Maximum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	522 --advntr-min-spanning ADVNTR_MIN_SPANNING
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	523 Minimum spanning read count (SR field)
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	524 --advntr-min-flanking ADVNTR_MIN_FLANKING
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	525 Minimum flanking read count (FR field)
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	526 --advntr-min-ML ADVNTR_MIN_ML
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	527 Minimum value of maximum likelihood (ML field)
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	528
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	529 Call-level filters specific to ExpansionHunter output:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	530 --eh-min-ADFL EH_MIN_ADFL
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	531 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	532 --eh-min-ADIR EH_MIN_ADIR
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	533 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	534 --eh-min-ADSP EH_MIN_ADSP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	535 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	536 --eh-min-call-LC EH_MIN_CALL_LC
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	537 Minimum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	538 --eh-max-call-LC EH_MAX_CALL_LC
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	539 Maximum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	540
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	541 Call-level filters specific to PopSTR output:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	542 --popstr-min-call-DP POPSTR_MIN_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	543 Minimum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	544 --popstr-max-call-DP POPSTR_MAX_CALL_DP
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	545 Maximum call coverage
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	546 --popstr-require-support POPSTR_REQUIRE_SUPPORT
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	547 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	548
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	549 Debugging parameters:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	550 --num-records NUM_RECORDS
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	551 Only process this many records
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	552 --die-on-warning 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	553 --verbose Print out extra info
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	554
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	555 Version:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	556 --version show program's version number and exit
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	557 </help>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	558
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 <citations>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	561 <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	562 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	563 year = {2020},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	564 title = {TRTools},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	565 publisher = {GitHub},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	566 journal = {GitHub repository},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	567 url = {https://github.com/gymreklab/trtools},
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	568 }
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	569 </citation>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	570 </citations>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e" michal_klinka parents: diff changeset	571 </tool>

Mercurial > repos > michal_klinka > trtools

annotate DumpSTR/dumpSTR.xml @ 0:ecf8c4f9f8ba draft