gatk4_mutect2: macros.xml annotate

annotate macros.xml @ 8:55e8a08e39e1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31

author	iuc
date	Tue, 03 Feb 2026 18:50:29 +0000
parents	04253ade1697
children

rev	line source
0 269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	1 <?xml version="1.0"?>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	2 <macros>
8 55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	3 <token name="@TOOL_VERSION@">4.6.2.0</token>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	4 <token name="@VERSION_SUFFIX@">0</token>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	5 <token name="@PROFILE@">24.1</token>
0 269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	6
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	7 <xml name="requirements">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	8 <requirements>
8 55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	9 <requirement type="package" version="@TOOL_VERSION@">gatk4</requirement>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	10 <requirement type="package" version="1.11">tabix</requirement>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	11 <requirement type="package" version="1.23">samtools</requirement>
0 269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	12 <yield />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	13 </requirements>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	14 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	15
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	16 <!--Hacky way to determine GATK version, for display in tool info-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	17 <xml name="version_cmd">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	18 <version_command>gatk SortSam --version 2>&1 \| grep Version \| cut -d ':' -f 2</version_command>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	19 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	20
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	21 <!--Define sections that parameters could exist within.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	22 <template name="set_sections">
1 09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516" iuc parents: 0 diff changeset	23 #set global $sections = ['', 'optional.', 'advanced.', 'deprecated.']
0 269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	24 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	25
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	26 <!--Reference genome handling-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	27 <!--One template each for the different reference genome parameter names.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	28 <!--TODO: Can the reference parameters all be the same?-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	29 <xml name="ref_sel">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	30 <conditional name="reference_source">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	31 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	32 <option value="cached">Locally cached</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	33 <option value="history">History</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	34 <option value="no_ref" selected="true">Do not pass</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	35 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	36 <when value="cached">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	37 <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	38 <options from_data_table="all_fasta" >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	39 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	40 </options>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	41 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	42 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	43 <when value="history">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	44 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	45 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	46 <when value="no_ref" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	47 </conditional>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	48 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	49
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	50 <template name="ref_opts">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	51 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	52 #if $varExists($sect + "reference_source.reference_source_selector")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	53 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	54 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	55 --reference $getVar($sect + "reference_source.reference_sequence.fields.path")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	56 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	57 --reference reference.fa
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	58 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	59 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	60 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	61 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	62 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	63
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	64 <template name="picard_ref_opts">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	65 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	66 #if $varExists($sect + "reference_source.reference_source_selector")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	67 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	68 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	69 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	70 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	71 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	72 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	73 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	74 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	75 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	76 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	77
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	78 <template name="picard_ref_opts_plain">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	79 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	80 #if $varExists($sect + "reference_source.reference_source_selector")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	81 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	82 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	83 --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	84 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	85 --REFERENCE $getVar($sect + "reference_source.reference_sequence")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	86 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	87 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	88 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	89 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	90 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	91
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	92 <template name="ref_opts_input">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	93 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	94 #if $varExists($sect + "reference_source.reference_source_selector")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	95 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	96 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	97 --input $getVar($sect + "reference_source.reference_sequence.fields.path")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	98 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	99 --input $getVar($sect + "reference_source.reference_sequence")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	100 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	101 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	102 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	103 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	104 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	105
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	106
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	107 <!--Interval Macros-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	108 <template name="gatk_ints_chth">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	109 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	110 #if $varExists($sect + "ival_type.ival_type_sel")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	111 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	112 #if $varExists($sect + "ival_type.intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	113 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	114 --intervals intervals.interval_list
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	115 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	116 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	117 --intervals intervals.bed
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	118 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	119 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	120 --intervals intervals.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	121 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	122 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	123 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	124 #if $varExists($sect + "ival_type.intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	125 --intervals $getVar($sect + "ival_type.intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	126 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	127 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	128 #if $varExists($sect + "ival_type.interval_padding")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	129 --interval-padding $getVar($sect + "ival_type.interval_padding")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	130 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	131 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	132 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	133 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	134
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	135
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	136 <template name="pre_gatk_ints_chth"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	137 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	138 #if $varExists($sect + "ival_type.ival_type_sel")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	139 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	140 #if $varExists($sect + "ival_type.intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	141 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	142 ln -s $getVar($sect + "ival_type.intervals") intervals.interval_list &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	143 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	144 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	145 ln -s $getVar($sect + "ival_type.intervals") intervals.bed &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	146 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	147 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	148 ln -s $getVar($sect + "ival_type.intervals") intervals.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	149 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	150 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	151 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	152 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	153 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	154 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	155
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	156 <xml name="gatk_ints">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	157 <conditional name="ival_type">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	158 <param name="ival_type_sel" type="select" label="Choose Genomic Interval Source">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	159 <option value="ival_file" selected="true">Interval File</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	160 <option value="ival_text" selected="false">Interval Text Input</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	161 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	162 <when value="ival_file">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	163 <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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	164 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	165 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	166 <when value="ival_text">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	167 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	168 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	169 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	170 </conditional>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	171 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	172
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	173
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	174 <!--Exclude Intervals-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	175 <xml name="gatk_excl_ints">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	176 <conditional name="excl_ival_type">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	177 <param name="excl_ival_type_sel" type="select" label="Choose Genomic Interval Exclusion Source">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	178 <option value="excl_ival_file" selected="true">Exclude Interval File</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	179 <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	180 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	181 <when value="excl_ival_file">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	182 <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"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	183 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	184 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	185 <when value="excl_ival_text">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	186 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	187 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	188 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	189 </conditional>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	190 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	191
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	192 <template name="gatk_excl_ints_chth">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	193 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	194 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	195 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "ival_file"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	196 #if $varExists($sect + "excl_ival_type.exclude_intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	197 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	198 --exclude-intervals excl_intervals.interval_list
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	199 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	200 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	201 --exclude-intervals excl_intervals.bed
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	202 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	203 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	204 --exclude-intervals excl_intervals.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	205 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	206 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	207 #elif $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_text"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	208 #if $varExists($sect + "excl_ival_type.exclude_intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	209 --exclude-intervals $getVar($sect + "excl_ival_type.exclude_intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	210 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	211 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	212 #pass
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	213 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	214 #if $varExists($sect + "excl_ival_type.interval_exclusion_padding")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	215 --interval-exclusion-padding $getVar($sect + "excl_ival_type.interval_exclusion_padding")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	216 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	217 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	218 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	219 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	220
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	221 <template name="pre_gatk_excl_ints_chth"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	222 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	223 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	224 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_file"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	225 #if $varExists($sect + "excl_ival_type.exclude_intervals")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	226 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	227 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.interval_list &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	228 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	229 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	230 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.bed &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	231 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	232 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	233 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	234 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	235 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	236 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	237 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	238 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	239 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	240
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	241 <!--Sequence dictionary selection options for Picard type tools-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	242 <template name="picard_seqdict_opts">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	243 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	244 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	245 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	246 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	247 #set seq_dict_loc = ''.join($getVar($sect + seqdict_source.seqdict_sequence).fields.path.split('.')[:-1]) + '.dict'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	248 --SEQUENCE_DICTIONARY $seq_dict_loc
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	249 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	250 --SEQUENCE_DICTIONARY $getVar($sect + "seqdict_source.seqdict_sequence")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	251 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	252 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	253 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	254 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	255 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	256
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	257 <template name="gatk_seqdict">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	258 #for $sect in $sections
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	259 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	260 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	261 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	262 #set $seq_dict_loc = ''.join($getVar($sect + "seqdict_source.seqdict_sequence").fields.path.split('.')[:-1]) + '.dict'
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	263 --sequence-dictionary $seq_dict_loc
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	264 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	265 --sequence-dictionary $getVar($sect + "seqdict_source.seqdict_sequence")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	266 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	267 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	268 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	269 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	270 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	271
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	272 <xml name="seq_dict_sel">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	273 <conditional name="seqdict_source">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	274 <param name="seqdict_source_selector" type="select" label="Choose the source for the sequence dictionary">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	275 <option value="cached">Locally cached</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	276 <option value="history">History</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	277 <option value="no_seq_dict" selected="true">Do not pass</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	278 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	279 <when value="cached">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	280 <param name="seqdict_sequence" type="select" label="Sequence Dictionary" help="Sequence dictionary file." >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	281 <options from_data_table="all_fasta" >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	282 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	283 </options>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	284 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	285 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	286 <when value="history">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	287 <param name="seqdict_sequence" type="data" format="txt" label="Sequence Dictionary" help="Sequence dictionary file. Must be in dict format." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	288 </when>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	289 <when value="no_seq_dict" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	290 </conditional>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	291 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	292
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	293 <!--Output goes to stdout, no output parameter exists.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	294 <template name="stdout_to_output">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	295 > output.txt
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	296 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	297
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	298 <xml name="stdout_to_output_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	299 <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	300 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	301
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	302 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	303 <template name="gatk_input_multi"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	304 #for $num, $file in enumerate($variant)
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	305 #if $file.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	306 --variant input${num}.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	307 #elif $file.is_of_type("txt")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	308 --variant input${num}.list
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	309 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	310 --variant input${num}.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	311 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	312 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	313 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	314
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	315 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	316 <template name="gatk_input_single"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	317 #if $variant.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	318 --variant input${num}.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	319 #elif $variant.is_of_type("txt")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	320 --variant input${num}.list
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	321 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	322 --variant input${num}.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	323 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	324 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	325
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	326 <template name="gatk_tabix_multi"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	327 #for $num, $file in enumerate($variant)
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	328 #set datatype = $file.datatype
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	329 #if $file.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	330 ln -s $file input${num}.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	331 tabix input${num}.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	332 #elif $file.is_of_type("txt")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	333 ln -s $file input${num}.list &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	334 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	335 ln -s $file input${num}.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	336 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	337 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	338 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	339
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	340 <xml name="vcf_input_params_multi">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	341 <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)"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	342 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	343
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	344
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	345
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	346 <!--ABOVE HAS BEEN REVIEWED-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	347
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	348
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	349
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	350
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	351
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	352
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	353
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	354
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	355
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	356
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	357 <!--{-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	358 <!--"summary": "BAM/SAM/CRAM file containing reads",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	359 <!--"name": "--input",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	360 <!--"synonyms": "-I",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	361 <!--"type": "List[String]",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	362 <!--"required": "yes",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	363 <!--"fulltext": "",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	364 <!--"defaultValue": "[]",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	365 <!--"minValue": "NA",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	366 <!--"maxValue": "NA",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	367 <!--"minRecValue": "NA",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	368 <!--"maxRecValue": "NA",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	369 <!--"kind": "required",-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	370 <!--"options": []-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	371 <!--},-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	372 <!--Required BAM input, GATK tool, may be specified multiple times.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	373 <!--BAM should be indexed on the fly.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	374 <!--Parameter is required, so is not contained within a section.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	375 <!--Only decriptor that makes this unique for all input parameters is the summary field.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	376 <!--{'pre_chth': ['bam_index_pre_chth'],-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	377 <!--'main_chth': ['picard_bam_input'],-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	378 <!--'main_xml': ['gatk_bam_req_params']}},-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	379
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	380
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	381
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	382
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	383
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	384
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	385
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	386
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	387
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	388
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	389
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	390
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	391
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	392 <!--Macros for multiple input tools. List[File] in GATK json.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	393 <template name="vcf_tabix_multi"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	394 #for $num, $file in enumerate($input)
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	395 #set datatype = $file.datatype
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	396 #if $file.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	397 ln -s $file input${num}.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	398 tabix input${num}.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	399 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	400 ln -s $file input${num}.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	401 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	402 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	403 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	404
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	405 <template name="vcf_input_multi_picard"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	406 #for $num, $file in enumerate($input)
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	407 #if $file.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	408 --INPUT input${num}.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	409 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	410 --INPUT input${num}.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	411 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	412 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	413 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	414
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	415 <template name="vcf_input_multi"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	416 #for $num, $file in enumerate($input)
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	417 #if $file.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	418 --input input${num}.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	419 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	420 --input input${num}.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	421 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	422 #end for
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	423 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	424
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	425
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	426 <!--Picard single input tools-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	427 <template name="vcf_tabix"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	428 #set datatype = $input.datatype
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	429 #if $input.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	430 ln -s $input input.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	431 tabix input.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	432 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	433 ln -s $input input.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	434 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	435 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	436
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	437 <template name="gatk_tabix"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	438 #set datatype = $variant.datatype
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	439 #if $variant.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	440 ln -s $variant input.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	441 tabix input.vcf.gz &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	442 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	443 ln -s $variant input.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	444 gatk IndexFeatureFile -F input.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	445 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	446 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	447
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	448 <template name="vcf_input_picard"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	449 #if $input.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	450 --INPUT input.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	451 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	452 --INPUT input.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	453 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	454 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	455
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	456 <template name="vcf_input"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	457 #if $input.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	458 --input input.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	459 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	460 --input input.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	461 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	462 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	463
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	464 <template name="gatk_input"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	465 #if $variant.is_of_type("vcf_bgzip")
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	466 --variant input.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	467 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	468 --variant input.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	469 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	470 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	471
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	472 <template name="gatk_gvcf_tabix"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	473 #if $variant
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	474 ln -s $variant input.g.vcf &&
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	475 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	476 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	477
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	478 <template name="gatk_gvcf_input"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	479 --variant input.g.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	480 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	481
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	482 <xml name="gatk_gvcf_input_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	483 <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	484 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	485
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	486 <xml name="vcf_input_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	487 <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)"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	488 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	489
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	490 <xml name="gatk_vcf_input_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	491 <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	492 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	493
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	494 <xml name="gatk_vcf_input_params_multi">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	495 <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."/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	496 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	497
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	498 <xml name="gatk_req_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	499 <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	500 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	501
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	502 <!--HDF5 Inputs-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	503
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	504 <xml name="hdf5_input">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	505 <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)." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	506 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	507
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	508 <template name="hdf5_input_chth"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	509 --input "${input}"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	510 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	511
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	512 <template name="hdf5_output_chth">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	513 --output "${output}"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	514 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	515
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	516 <xml name="hdf5_output">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	517 <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	518 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	519
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	520 <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	521 <!--${SAMPLE}.cr.seg-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	522 <!--${SAMPLE}.modelFinal.seg-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	523 <template name="modelsegments_chth"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	524 --output "."
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	525 --output-prefix "modelsegments"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	526 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	527
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	528 <xml name="modelsegments_output">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	529 <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	530 <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	531 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	532
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	533 <!--deltaMAD.txt-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	534 <!--denoisedLimit4.png-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	535 <!--denoisedMAD.txt-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	536 <!--denoised.png-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	537 <!--scaledDeltaMAD.txt-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	538 <!--modeled.png-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	539 <!--standardizedMAD.txt-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	540
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	541 <template name="plotmodeledsegments_chth"><![CDATA[
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	542 --output "."
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	543 --output-prefix "plotmodeledsegments"
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	544 ]]></template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	545
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	546 <xml name="plotmodeledsegments_output">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	547 <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	548 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	549
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	550 <!--Common Picard options-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	551 <template name="picard_opts">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	552 #if $picard_adv.arguments_file
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	553 --arguments_file ${picard_adv.arguments_file}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	554 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	555 --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	556 #if $picard_adv.GA4GH_CLIENT_SECRETS
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	557 --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	558 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	559 --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	560 --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	561 --VERBOSITY ${picard_adv.VERBOSITY}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	562 ${picard_adv.CREATE_MD5_FILE}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	563 ${picard_adv.USE_JDK_DEFLATER}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	564 ${picard_adv.USE_JDK_INFLATER}
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	565 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	566
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	567 <xml name="picard_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	568 <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	569 <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" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	570 <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)." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	571 <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." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	572 <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	573 <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." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	574 <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." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	575 <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" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	576 <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" />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	577 <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." >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	578 <option value="STRICT" selected="true">STRICT</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	579 <option value="LENIENT" selected="false">LENIENT</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	580 <option value="SILENT" selected="false">SILENT</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	581 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	582 <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	583 <option value="ERROR" selected="false">ERROR</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	584 <option value="WARNING" selected="false">WARNING</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	585 <option value="INFO" selected="true">INFO</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	586 <option value="DEBUG" selected="false">DEBUG</option>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	587 </param>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	588 </section>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	589 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	590
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	591 <!--Provides option to create gzipped output for VCF files-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	592 <xml name="gzip_vcf_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	593 <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." />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	594 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	595
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	596 <!--Output related Picard options-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	597 <xml name="gzip_vcf_output_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	598 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	599 <filter>not gzipped_output</filter>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	600 </data>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	601 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	602 <filter>gzipped_output</filter>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	603 </data>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	604 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	605
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	606
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	607 <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	608 <template name="picard_vcf_output_opts">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	609 #if $gzipped_output
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	610 --OUTPUT output.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	611 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	612 --OUTPUT output.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	613 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	614 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	615
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	616 <template name="vcf_output_opts">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	617 #if $gzipped_output
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	618 --output output.vcf.gz
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	619 #else
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	620 --output output.vcf
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	621 #end if
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	622 </template>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	623
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	624 <xml name="picard_output_params">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	625 <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	626 <filter>picard_adv['CREATE_MD5_FILE']</filter>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	627 </data>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	628 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	629
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	630
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	631 <!--<template name="ref_opts">-->
1 09393225f90f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit 5d2fd48454149b3cfa39aaba71e3b19f89087516" iuc parents: 0 diff changeset	632 <!--#set $sections = ['optional','advanced','deprecated','']-->
0 269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	633 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	634 <!--#for $sect in $sections-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	635 <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	636 <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	637 <!--#if $sect.reference_source.reference_source_selector != "history"-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	638 <!----reference ${sect.reference_source.reference_sequence.fields.path}-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	639 <!--#else-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	640 <!----reference ${sect.reference_source.reference_sequence}-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	641 <!--#end if-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	642 <!--#end if-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	643 <!--#end if-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	644 <!--#end for-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	645 <!--</template>-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	646
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	647
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	648 <!--<template name="ref_opts_opt">-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	649 <!--#if $optional.reference_source.reference_source_selector != "no_ref"-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	650 <!--#if $optional.reference_source.reference_source_selector != "history"-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	651 <!----reference ${optional.reference_source.reference_sequence.fields.path}-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	652 <!--#else-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	653 <!----reference ${optional.reference_source.reference_sequence}-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	654 <!--#end if-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	655 <!--#end if-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	656 <!--</template>-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	657
8 55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	658 <token name="@GATK_LINK_REF@"><![CDATA[
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	659 ## 1. Link Reference Genome
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	660 #if $reference_source.reference_source_selector == "history":
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	661 ln -s '$reference_source.reference_sequence' reference.fa &&
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	662 samtools faidx reference.fa &&
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	663 #else:
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	664 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	665 ln -s '${reference_source.reference_sequence.fields.path}.fai' reference.fa.fai &&
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	666 #end if
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	667
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	668 ## Ensure dictionary exists
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	669 gatk CreateSequenceDictionary -R reference.fa &&
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	670 ]]></token>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	671
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	672 <xml name="gatk_ref_source">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	673 <conditional name="reference_source">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	674 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	675 <option value="cached">Locally cached</option>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	676 <option value="history" selected="true">History</option>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	677 </param>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	678 <when value="cached">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	679 <param name="reference_sequence" type="select" label="Reference" help="Select reference genome">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	680 <options from_data_table="all_fasta" />
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	681 </param>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	682 </when>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	683 <when value="history">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	684 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Select reference genome from history" />
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	685 </when>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	686 </conditional>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	687 </xml>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	688
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	689 <xml name="gatk_param_intervals">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	690 <param name="intervals" argument="-L" type="data" format="picard_interval_list" optional="true" label="Interval List" help="One or more genomic intervals over which to operate." />
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	691 </xml>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	692
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	693 <xml name="gatk_param_known_sites">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	694 <param argument="--known-sites" type="data" format="vcf_bgzip" multiple="true" label="Known Sites" help="VCF file(s) (e.g., dbSNP, Mills) masking known sites." />
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	695 </xml>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	696
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	697 <xml name="gatk_param_use_original_qualities">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	698 <param argument="--use-original-qualities" type="boolean" truevalue="--use-original-qualities" falsevalue="" checked="true" label="Use Original Qualities" help="Use the OQ tag if present." />
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	699 </xml>
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	700
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	701 <xml name="gatk_param_add_output_sam_program_record">
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	702 <param argument="--add-output-sam-program-record" type="boolean" truevalue="--add-output-sam-program-record" falsevalue="" checked="true" label="Add Output SAM Program Record" help="Adds an extra PG tag to the header." />
55e8a08e39e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31 iuc parents: 6 diff changeset	703 </xml>
0 269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	704
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	705 <!--Citations-->
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	706 <xml name="citations">
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	707 <citation type="doi">10.1101/gr.107524.110</citation>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	708 <citation type="doi">10.1038/ng.806</citation>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	709 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	710 <citation type="doi">10.1101/201178</citation>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	711 <yield />
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	712 </xml>
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	713
269335b7ff6e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/gatk4 commit f9d04b348a43a799ab1624d3a7b211aab55ae522" iuc parents: diff changeset	714 </macros>

Mercurial > repos > iuc > gatk4_mutect2

annotate macros.xml @ 8:55e8a08e39e1 draft default tip