gatk4: macros_filtermutectcalls.xml annotate

annotate macros_filtermutectcalls.xml @ 2:646e6943bcd2 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339

author	artbio
date	Sun, 15 Oct 2023 12:06:24 +0000
parents	c51c08cc9fcc
children

rev	line source
0 c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	1 <?xml version="1.0"?>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	2 <macros>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	3 <token name="@VERSION@">4.1.7.0</token>
2 646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339 artbio parents: 0 diff changeset	4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy2</token>
0 c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	5
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	6 <xml name="requirements">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	7 <requirements>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	8 <requirement type="package" version="@VERSION@">gatk4</requirement>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	9 <requirement type="package" version="0.2.5">tabix</requirement>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	10 <requirement type="package" version="1.9">samtools</requirement>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	11 <yield />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	12 </requirements>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	13 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	14
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	15 <!--Hacky way to determine GATK version, for display in tool info-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	16 <xml name="version_cmd">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	17 <version_command>gatk SortSam --version 2>&1 \| grep Version \| cut -d ':' -f 2</version_command>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	18 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	19
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	20 <!--Define sections that parameters could exist within.-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	21 <template name="set_sections">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	22 #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	23 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	24
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	25 <!--Reference genome handling-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	26 <!--One template each for the different reference genome parameter names.-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	27 <!--TODO: Can the reference parameters all be the same?-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	28 <xml name="ref_sel">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	29 <conditional name="reference_source">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	30 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	31 <option value="cached">Locally cached</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	32 <option value="history">History</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	33 <option value="no_ref" selected="true">Do not pass</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	34 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	35 <when value="cached">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	36 <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	37 <options from_data_table="all_fasta" >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	38 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	39 </options>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	40 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	41 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	42 <when value="history">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	43 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	44 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	45 <when value="no_ref" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	46 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	47 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	48
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	49 <template name="ref_opts">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	50 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	51 #if $varExists($sect + "reference_source.reference_source_selector")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	52 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	53 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	54 --reference $getVar($sect + "reference_source.reference_sequence.fields.path")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	55 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	56 --reference reference.fa
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	57 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	58 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	59 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	60 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	61 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	62
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	63 <template name="picard_ref_opts">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	64 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	65 #if $varExists($sect + "reference_source.reference_source_selector")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	66 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	67 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	68 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	69 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	70 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	71 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	72 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	73 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	74 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	75 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	76
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	77 <template name="picard_ref_opts_plain">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	78 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	79 #if $varExists($sect + "reference_source.reference_source_selector")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	80 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	81 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	82 --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	83 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	84 --REFERENCE $getVar($sect + "reference_source.reference_sequence")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	85 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	86 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	87 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	88 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	89 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	90
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	91 <template name="ref_opts_input">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	92 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	93 #if $varExists($sect + "reference_source.reference_source_selector")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	94 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	95 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	96 --input $getVar($sect + "reference_source.reference_sequence.fields.path")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	97 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	98 --input $getVar($sect + "reference_source.reference_sequence")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	99 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	100 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	101 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	102 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	103 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	104
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	105
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	106 <!--Interval Macros-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	107 <template name="gatk_ints_chth">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	108 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	109 #if $varExists($sect + "ival_type.ival_type_sel")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	110 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	111 #if $varExists($sect + "ival_type.intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	112 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	113 --intervals intervals.interval_list
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	114 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	115 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	116 --intervals intervals.bed
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	117 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	118 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	119 --intervals intervals.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	120 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	121 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	122 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	123 #if $varExists($sect + "ival_type.intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	124 --intervals $getVar($sect + "ival_type.intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	125 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	126 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	127 #if $varExists($sect + "ival_type.interval_padding")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	128 --interval-padding $getVar($sect + "ival_type.interval_padding")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	129 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	130 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	131 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	132 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	133
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	134
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	135 <template name="pre_gatk_ints_chth"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	136 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	137 #if $varExists($sect + "ival_type.ival_type_sel")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	138 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	139 #if $varExists($sect + "ival_type.intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	140 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	141 ln -s $getVar($sect + "ival_type.intervals") intervals.interval_list &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	142 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	143 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	144 ln -s $getVar($sect + "ival_type.intervals") intervals.bed &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	145 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	146 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	147 ln -s $getVar($sect + "ival_type.intervals") intervals.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	148 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	149 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	150 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	151 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	152 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	153 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	154
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	155 <xml name="gatk_ints">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	156 <conditional name="ival_type">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	157 <param name="ival_type_sel" type="select" label="Choose Genomic Interval Source">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	158 <option value="ival_file" selected="true">Interval File</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	159 <option value="ival_text" selected="false">Interval Text Input</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	160 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	161 <when value="ival_file">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	162 <param name="intervals" argument="--intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Intervals File" help="One or more genomic intervals over which to operate"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	163 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	164 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	165 <when value="ival_text">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	166 <param name="intervals" argument="--intervals" type="text" optional="true" label="Intervals Text Input" help="One or more genomic intervals over which to operate. Enter in chrom:start-stop format."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	167 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	168 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	169 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	170 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	171
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	172
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	173 <!--Exclude Intervals-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	174 <xml name="gatk_excl_ints">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	175 <conditional name="excl_ival_type">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	176 <param name="excl_ival_type_sel" type="select" label="Choose Genomic Interval Exclusion Source">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	177 <option value="excl_ival_file" selected="true">Exclude Interval File</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	178 <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	179 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	180 <when value="excl_ival_file">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	181 <param name="exclude_intervals" argument="--exclude-intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Exclude Intervals File" help="One or more genomic intervals to exclude from processing"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	182 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	183 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	184 <when value="excl_ival_text">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	185 <param name="exclude_intervals" argument="--exclude-intervals" type="text" optional="true" label="Exclude Intervals Text Input" help="One or more genomic intervals to exclude from processing. Enter in chrom:start-stop format."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	186 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	187 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	188 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	189 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	190
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	191 <template name="gatk_excl_ints_chth">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	192 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	193 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	194 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "ival_file"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	195 #if $varExists($sect + "excl_ival_type.exclude_intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	196 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	197 --exclude-intervals excl_intervals.interval_list
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	198 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	199 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	200 --exclude-intervals excl_intervals.bed
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	201 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	202 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	203 --exclude-intervals excl_intervals.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	204 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	205 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	206 #elif $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_text"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	207 #if $varExists($sect + "excl_ival_type.exclude_intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	208 --exclude-intervals $getVar($sect + "excl_ival_type.exclude_intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	209 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	210 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	211 #pass
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	212 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	213 #if $varExists($sect + "excl_ival_type.interval_exclusion_padding")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	214 --interval-exclusion-padding $getVar($sect + "excl_ival_type.interval_exclusion_padding")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	215 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	216 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	217 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	218 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	219
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	220 <template name="pre_gatk_excl_ints_chth"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	221 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	222 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	223 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_file"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	224 #if $varExists($sect + "excl_ival_type.exclude_intervals")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	225 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	226 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.interval_list &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	227 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	228 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	229 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.bed &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	230 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	231 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	232 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	233 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	234 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	235 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	236 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	237 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	238 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	239
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	240 <!--Sequence dictionary selection options for Picard type tools-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	241 <template name="picard_seqdict_opts">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	242 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	243 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	244 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	245 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	246 #set seq_dict_loc = ''.join($getVar($sect + seqdict_source.seqdict_sequence).fields.path.split('.')[:-1]) + '.dict'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	247 --SEQUENCE_DICTIONARY $seq_dict_loc
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	248 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	249 --SEQUENCE_DICTIONARY $getVar($sect + "seqdict_source.seqdict_sequence")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	250 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	251 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	252 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	253 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	254 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	255
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	256 <template name="gatk_seqdict">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	257 #for $sect in $sections
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	258 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	259 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	260 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	261 #set $seq_dict_loc = ''.join($getVar($sect + "seqdict_source.seqdict_sequence").fields.path.split('.')[:-1]) + '.dict'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	262 --sequence-dictionary $seq_dict_loc
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	263 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	264 --sequence-dictionary $getVar($sect + "seqdict_source.seqdict_sequence")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	265 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	266 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	267 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	268 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	269 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	270
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	271 <xml name="seq_dict_sel">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	272 <conditional name="seqdict_source">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	273 <param name="seqdict_source_selector" type="select" label="Choose the source for the sequence dictionary">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	274 <option value="cached">Locally cached</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	275 <option value="history">History</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	276 <option value="no_seq_dict" selected="true">Do not pass</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	277 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	278 <when value="cached">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	279 <param name="seqdict_sequence" type="select" label="Sequence Dictionary" help="Sequence dictionary file." >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	280 <options from_data_table="all_fasta" >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	281 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	282 </options>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	283 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	284 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	285 <when value="history">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	286 <param name="seqdict_sequence" type="data" format="txt" label="Sequence Dictionary" help="Sequence dictionary file. Must be in dict format." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	287 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	288 <when value="no_seq_dict" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	289 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	290 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	291
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	292 <!--Output goes to stdout, no output parameter exists.-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	293 <template name="stdout_to_output">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	294 > output.txt
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	295 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	296
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	297 <xml name="stdout_to_output_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	298 <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	299 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	300
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	301 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	302 <template name="gatk_input_multi"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	303 #for $num, $file in enumerate($variant)
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	304 #if $file.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	305 --variant input${num}.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	306 #elif $file.is_of_type("txt")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	307 --variant input${num}.list
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	308 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	309 --variant input${num}.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	310 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	311 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	312 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	313
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	314 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	315 <template name="gatk_input_single"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	316 #if $variant.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	317 --variant input${num}.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	318 #elif $variant.is_of_type("txt")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	319 --variant input${num}.list
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	320 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	321 --variant input${num}.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	322 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	323 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	324
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	325 <template name="gatk_tabix_multi"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	326 #for $num, $file in enumerate($variant)
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	327 #set datatype = $file.datatype
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	328 #if $file.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	329 ln -s $file input${num}.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	330 tabix input${num}.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	331 #elif $file.is_of_type("txt")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	332 ln -s $file input${num}.list &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	333 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	334 ln -s $file input${num}.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	335 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	336 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	337 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	338
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	339 <xml name="vcf_input_params_multi">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	340 <param name="input" type="data" multiple="true" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	341 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	342
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	343
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	344 <!--Macros for multiple input tools. List[File] in GATK json.-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	345 <template name="vcf_tabix_multi"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	346 #for $num, $file in enumerate($input)
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	347 #set datatype = $file.datatype
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	348 #if $file.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	349 ln -s $file input${num}.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	350 tabix input${num}.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	351 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	352 ln -s $file input${num}.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	353 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	354 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	355 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	356
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	357 <template name="vcf_input_multi_picard"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	358 #for $num, $file in enumerate($input)
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	359 #if $file.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	360 --INPUT input${num}.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	361 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	362 --INPUT input${num}.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	363 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	364 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	365 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	366
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	367 <template name="vcf_input_multi"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	368 #for $num, $file in enumerate($input)
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	369 #if $file.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	370 --input input${num}.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	371 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	372 --input input${num}.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	373 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	374 #end for
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	375 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	376
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	377
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	378 <!--Picard single input tools-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	379 <template name="vcf_tabix"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	380 #set datatype = $input.datatype
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	381 #if $input.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	382 ln -s $input input.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	383 tabix input.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	384 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	385 ln -s $input input.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	386 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	387 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	388
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	389 <template name="gatk_tabix"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	390 #set datatype = $variant.datatype
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	391 #if $variant.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	392 ln -s $variant input.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	393 tabix input.vcf.gz &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	394 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	395 ln -s $variant input.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	396 gatk IndexFeatureFile -F input.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	397 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	398 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	399
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	400 <template name="vcf_input_picard"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	401 #if $input.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	402 --INPUT input.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	403 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	404 --INPUT input.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	405 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	406 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	407
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	408 <template name="vcf_input"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	409 #if $input.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	410 --input input.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	411 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	412 --input input.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	413 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	414 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	415
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	416 <template name="gatk_input"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	417 #if $variant.is_of_type("vcf_bgzip")
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	418 --variant input.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	419 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	420 --variant input.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	421 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	422 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	423
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	424 <template name="gatk_gvcf_tabix"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	425 #if $variant
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	426 ln -s $variant input.g.vcf &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	427 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	428 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	429
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	430 <template name="gatk_gvcf_input"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	431 --variant input.g.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	432 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	433
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	434 <xml name="gatk_gvcf_input_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	435 <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	436 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	437
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	438 <xml name="vcf_input_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	439 <param name="input" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	440 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	441
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	442 <xml name="gatk_vcf_input_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	443 <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	444 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	445
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	446 <xml name="gatk_vcf_input_params_multi">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	447 <param name="variant" type="data" multiple="true" format="vcf,vcf_bgzip,txt" label="Input VCF file(s)" help="A VCF file containing variants or a list of VCFs. Can be specified multiple times."/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	448 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	449
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	450 <xml name="gatk_req_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	451 <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	452 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	453
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	454 <!--HDF5 Inputs-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	455
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	456 <xml name="hdf5_input">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	457 <param name="input" type="data" format="h5,tabular" label="Input TSV or HDF5" help="Input TSV or HDF5 file containing integer read counts in genomic intervals for a single case sample (output of CollectReadCounts)." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	458 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	459
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	460 <template name="hdf5_input_chth"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	461 --input "${input}"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	462 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	463
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	464 <template name="hdf5_output_chth">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	465 --output "${output}"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	466 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	467
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	468 <xml name="hdf5_output">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	469 <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	470 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	471
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	472 <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	473 <!--${SAMPLE}.cr.seg-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	474 <!--${SAMPLE}.modelFinal.seg-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	475 <template name="modelsegments_chth"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	476 --output "."
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	477 --output-prefix "modelsegments"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	478 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	479
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	480 <xml name="modelsegments_output">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	481 <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	482 <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	483 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	484
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	485 <!--deltaMAD.txt-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	486 <!--denoisedLimit4.png-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	487 <!--denoisedMAD.txt-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	488 <!--denoised.png-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	489 <!--scaledDeltaMAD.txt-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	490 <!--modeled.png-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	491 <!--standardizedMAD.txt-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	492
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	493 <template name="plotmodeledsegments_chth"><![CDATA[
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	494 --output "."
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	495 --output-prefix "plotmodeledsegments"
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	496 ]]></template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	497
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	498 <xml name="plotmodeledsegments_output">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	499 <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	500 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	501
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	502 <!--Common Picard options-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	503 <template name="picard_opts">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	504 #if $picard_adv.arguments_file
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	505 --arguments_file ${picard_adv.arguments_file}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	506 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	507 --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	508 #if $picard_adv.GA4GH_CLIENT_SECRETS
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	509 --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	510 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	511 --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	512 --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	513 --VERBOSITY ${picard_adv.VERBOSITY}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	514 ${picard_adv.CREATE_MD5_FILE}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	515 ${picard_adv.USE_JDK_DEFLATER}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	516 ${picard_adv.USE_JDK_INFLATER}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	517 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	518
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	519 <xml name="picard_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	520 <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	521 <param argument="--arguments_file" type="data" optional="true" format="txt" label="Arguments File" help="read one or more arguments files and add them to the command line" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	522 <param argument="--COMPRESSION_LEVEL" type="integer" optional="true" value="5" min="1" max="9" label="Compression Level" help="Compression level for all compressed files created (e.g. BAM and VCF)." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	523 <param argument="--CREATE_MD5_FILE" truevalue="--CREATE_MD5_FILE" falsevalue="" type="boolean" optional="true" checked="false" label="Create MD5 File" help="Whether to create an MD5 digest for any BAM or FASTQ files created." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	524 <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	525 <param argument="--MAX_RECORDS_IN_RAM" type="integer" optional="true" value="500000" label="Max Records In Ram" help="When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	526 <param argument="--TMP_DIR" type="text" optional="true" label="Tmp Dir" help="One or more directories with space available to be used by this program for temporary storage of working files. Keep in mind, you must be able to access this directory from either your user, or from the Galaxy user, depending on your configuration." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	527 <param argument="--USE_JDK_DEFLATER" truevalue="--USE_JDK_DEFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Deflater" help="Use the JDK Deflater instead of the Intel Deflater for writing compressed output" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	528 <param argument="--USE_JDK_INFLATER" truevalue="--USE_JDK_INFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Inflater" help="Use the JDK Inflater instead of the Intel Inflater for reading compressed input" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	529 <param argument="--VALIDATION_STRINGENCY" type="select" optional="true" label="Validation Stringency" help="Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded." >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	530 <option value="STRICT" selected="true">STRICT</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	531 <option value="LENIENT" selected="false">LENIENT</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	532 <option value="SILENT" selected="false">SILENT</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	533 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	534 <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	535 <option value="ERROR" selected="false">ERROR</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	536 <option value="WARNING" selected="false">WARNING</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	537 <option value="INFO" selected="true">INFO</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	538 <option value="DEBUG" selected="false">DEBUG</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	539 </param>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	540 </section>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	541 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	542
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	543 <!--Provides option to create gzipped output for VCF files-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	544 <xml name="gzip_vcf_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	545 <param name="gzipped_output" type="boolean" checked="true" label="GZIP Output?" help="If you would like gzipped output, check this box. In general, it would be preferable to do this, unless your downstream tool does not support handling of gzipped files." />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	546 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	547
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	548 <!--Output related Picard options-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	549 <xml name="gzip_vcf_output_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	550 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	551 <filter>not gzipped_output</filter>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	552 </data>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	553 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	554 <filter>gzipped_output</filter>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	555 </data>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	556 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	557
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	558
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	559 <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	560 <template name="picard_vcf_output_opts">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	561 #if $gzipped_output
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	562 --OUTPUT output.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	563 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	564 --OUTPUT output.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	565 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	566 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	567
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	568 <template name="vcf_output_opts">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	569 #if $gzipped_output
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	570 --output output.vcf.gz
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	571 #else
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	572 --output output.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	573 #end if
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	574 </template>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	575
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	576 <xml name="picard_output_params">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	577 <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	578 <filter>picard_adv['CREATE_MD5_FILE']</filter>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	579 </data>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	580 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	581
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	582
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	583 <!--Citations-->
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	584 <xml name="citations">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	585 <citation type="doi">10.1101/gr.107524.110</citation>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	586 <citation type="doi">10.1038/ng.806</citation>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	587 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	588 <citation type="doi">10.1101/201178</citation>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	589 <yield />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	590 </xml>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	591
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31" artbio parents: diff changeset	592 </macros>

Mercurial > repos > artbio > gatk4

annotate macros_filtermutectcalls.xml @ 2:646e6943bcd2 draft default tip