bcftools_isec: macros.xml annotate

annotate macros.xml @ 15:97d19c008d15 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit c45135e52ae5039e09272ac6f504d0ceb574aa70

author	iuc
date	Sat, 23 Jul 2022 13:53:08 +0000
parents	9ece72700ca9
children	5f27e814a119

rev	line source
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	1 <macros>
11 1fd4fd0c6ee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee" iuc parents: 10 diff changeset	2 <token name="@TOOL_VERSION@">1.10</token>
13 9ece72700ca9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163" iuc parents: 12 diff changeset	3 <xml name="bio_tools">
9ece72700ca9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163" iuc parents: 12 diff changeset	4 <xrefs>
9ece72700ca9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163" iuc parents: 12 diff changeset	5 <xref type="bio.tools">bcftools</xref>
9ece72700ca9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163" iuc parents: 12 diff changeset	6 </xrefs>
9ece72700ca9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163" iuc parents: 12 diff changeset	7 </xml>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	8 <xml name="requirements">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	9 <requirements>
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	10 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
11 1fd4fd0c6ee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee" iuc parents: 10 diff changeset	11 <requirement type="package" version="1.10">htslib</requirement>
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	12 <yield />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	13 </requirements>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	14 </xml>
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	15 <xml name="samtools_requirement">
11 1fd4fd0c6ee3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee" iuc parents: 10 diff changeset	16 <requirement type="package" version="1.10">samtools</requirement>
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	17 </xml>
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	18 <xml name="matplotlib_requirement">
13 9ece72700ca9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163" iuc parents: 12 diff changeset	19 <requirement type="package" version="3.4.3">matplotlib</requirement>
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	20 </xml>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	21 <xml name="version_command">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	22 <version_command>bcftools 2>&1 \| grep 'Version:'</version_command>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	23 </xml>
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	24
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	25 <xml name="citations">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	26 <citations>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	27 <citation type="doi">10.1093/bioinformatics/btp352</citation>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	28 <yield />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	29 </citations>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	30 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	31 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	32 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	33 <token name="@THREADS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	34 --threads \${GALAXY_SLOTS:-4}
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	35 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	36 <token name="@PREPARE_ENV@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	37 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	38 export BCFTOOLS_PLUGINS=`which bcftools \| sed 's,bin/bcftools,libexec/bcftools,'`;
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	39 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	40 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	41 <xml name="macro_input">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	43 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	44 <token name="@PREPARE_INPUT_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	45 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	46 ## May need to symlink input if there is an associated
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	47 #set $input_vcf = 'input.vcf.gz'
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	48 #if $input_file.is_of_type('vcf')
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	49 bgzip -c '$input_file' > $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	50 bcftools index $input_vcf &&
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	51 #elif $input_file.is_of_type('vcf_bgzip')
6 c803c34361e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3 iuc parents: 5 diff changeset	52 ln -s '$input_file' $input_vcf &&
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	53 #if $input_file.metadata.tabix_index:
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	54 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	55 #else
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	56 bcftools index $input_vcf &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	57 #end if
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	58 #elif $input_file.is_of_type('bcf')
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	59 #set $input_vcf = 'input.bcf'
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	60 ln -s '$input_file' $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	61 #if $input_file.metadata.bcf_index:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	62 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	63 #else
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	64 bcftools index $input_vcf &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	65 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	66 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	67 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	68 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	69 <token name="@INPUT_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	70 $input_vcf
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	71 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	72
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	73 <xml name="macro_inputs">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	74 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	75 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	76 <token name="@PREPARE_INPUT_FILES@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	77 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	78 ## May need to symlink input if there is an associated
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	79 #set $input_vcfs = []
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	80 #set $vcfs_list_file = 'vcfs_list'
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	81 #for (i, input_file) in enumerate($input_files):
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	82 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	83 #if $input_file.is_of_type('vcf')
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	84 bgzip -c '$input_file' > $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	85 bcftools index $input_vcf &&
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	86 #elif $input_file.is_of_type('vcf_bgzip')
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	87 ln -s '$input_file' $input_vcf &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	88 #if $input_file.metadata.tabix_index:
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	89 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	90 #else
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	91 bcftools index $input_vcf &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	92 #end if
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	93 #elif $input_file.is_of_type('bcf')
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	94 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	95 ln -s '$input_file' $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	96 #if $input_file.metadata.bcf_index:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	97 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	98 #else
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	99 bcftools index $input_vcf &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	100 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	101 #end if
1 ddf3dd241f7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06 iuc parents: 0 diff changeset	102 echo '$input_vcf' >> $vcfs_list_file &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	103 $input_vcfs.append($input_vcf)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	104 #end for
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	105 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	106 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	107 <token name="@INPUT_FILES@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	108 #echo ' '.join($input_vcfs)#
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	109 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	110 <token name="@INPUT_LIST_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	111 $vcfs_list_file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	112 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	113
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	114 <xml name="test_using_reference" token_select_from="history" token_ref="">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	115 <conditional name="reference_source">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	116 <param name="reference_source_selector" value="@SELECT_FROM@" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	117 <param name="fasta_ref" ftype="fasta" value="@REF@" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	118 </conditional>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	119 </xml>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	120
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	121 <xml name="macro_fasta_ref">
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	122 <conditional name="reference_source">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	123 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	124 <option value="cached">Use a built-in genome</option>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	125 <option value="history">Use a genome from the history</option>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	126 </param>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	127 <when value="cached">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	128 <param name="fasta_ref" type="select" label="Reference genome">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	129 <options from_data_table="fasta_indexes">
10 0d7d3de5ef5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 851f81495c875ac09d936537ffd2b32e6af2c8c5" iuc parents: 8 diff changeset	130 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" />
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	131 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	132 </options>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	133 </param>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	134 </when>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	135 <when value="history">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	136 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	137 </when>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	138 </conditional>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	139 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	140 <token name="@PREPARE_FASTA_REF@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	141 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	142 #set $input_fa_ref = None
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	143 #if 'fasta_ref' in $section and $section.fasta_ref:
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	144 #if 'reference_source_selector' in $section:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	145 #if str($section.reference_source_selector) == "history":
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	146 #set $input_fa_ref = 'ref.fa'
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	147 ln -s '$section.fasta_ref' $input_fa_ref &&
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	148 samtools faidx $input_fa_ref &&
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	149 #else:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	150 #set $input_fa_ref = str($section.fasta_ref.fields.path)
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	151 #end if
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	152 #end if
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	153 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	154 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	155 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	156 <token name="@FASTA_REF@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	157 #if $input_fa_ref is not None:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	158 --fasta-ref $input_fa_ref
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	159 #elif 'fasta_ref' in $section and $section.fasta_ref:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	160 --fasta-ref '${section.fasta_ref}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	161 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	162 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	163
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	164 <xml name="macro_AF_file">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	165 <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	166 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	167 <!-- This may need to bgzip and tabix the file -->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	168 <token name="@PREPARE_AF_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	169 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	170 #if 'AF_file' in $section and $section.AF_file:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	171 #pass
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	172 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	173 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	174 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	175 <token name="@AF_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	176 #if 'AF_file' in $section and $section.AF_file:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	177 --AF-file '${section.AF_file}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	178 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	179 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	180
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	181 <xml name="macro_estimate_AF">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	182 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	183 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	184 <token name="@ESTIMATE_AF@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	185 #if 'estimate_AF' in $section and $section.estimate_AF:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	186 --estimate-AF "${section.estimate_AF}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	187 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	188 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	189
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	190 <xml name="macro_exons_file">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	191 <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	192 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	193 <token name="@PREPARE_EXONS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	194 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	195 #set $exons_path = None
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	196 #if 'exons_file' in $section and $section.exons_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	197 #set $exons_path = 'exons_file.tab.gz'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	198 bgzip -c "$section.exons_file" > $exons_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	199 tabix -s 1 -b 2 -e 3 $exons_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	200 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	201 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	202 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	203 <token name="@EXONS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	204 #if 'exons_file' in $section and $section.exons_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	205 --exons $exons_path
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	206 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	207 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	208
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	209 <xml name="macro_ploidy_file">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	210 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	211 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	212 <token name="@PLOIDY_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	213 #if 'ploidy_file' in $section and $section.ploidy_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	214 --ploidy "${section.ploidy_file}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	215 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	216 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	217
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	218 <xml name="macro_collapse_opt_none">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	219 <option value="none">none - require the exact same set of alleles in all files</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	220 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	221 <xml name="macro_collapse_opt_id">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	222 <option value="id">id - only records with identical ID column are compatible. </option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	223 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	224 <xml name="macro_collapse">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	225 <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	226 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	227 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	228 <option value="both">both - indels and snps </option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	229 <option value="some">some - at least some of the ALTs must match</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	230 <option value="any">any - any combination of alleles</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	231 <yield/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	232 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	233 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	234 <token name="@COLLAPSE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	235 #if $section.collapse:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	236 --collapse ${section.collapse}
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	237 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	238 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	239
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	240 <xml name="macro_apply_filters">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	241 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	242 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	243 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	244 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	245 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	246 <token name="@APPLY_FILTERS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	247 #if $section.apply_filters:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	248 --apply-filters '${section.apply_filters}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	249 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	250 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	251
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	252 <xml name="macro_select_output_type">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	253 <param name="output_type" type="select">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	254 <option value="b">compressed BCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	255 <!-- no galaxy datatypes for these
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	256 <option value="u">uncompressed BCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	257 <option value="z">compressed VCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	258 -->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	259 <option value="v">uncompressed VCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	260 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	261 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	262 <token name="@OUTPUT_TYPE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	263 #if str($output_type) != "__none__":
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	264 --output-type '${output_type}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	265 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	266 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	267
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	268 <xml name="macro_vcf_output">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	269 <data name="output_file" format="vcf">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	270 <change_format>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	271 <when input="output_type" value="b" format="bcf" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	272 <when input="output_type" value="u" format="bcf" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	273 <when input="output_type" value="z" format="vcf_bgzip" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	274 <when input="output_type" value="v" format="vcf" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	275 </change_format>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	276 </data>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	277 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	278
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	279 <xml name="macro_invert_targets">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	280 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	281 label="Invert Targets"
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	282 help="inverts the query/filtering applied by the targets" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	283 </xml>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	284
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	285 <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	286 <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	287 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	288 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	289 </param>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	290 <param name="start" type="text" label="@LABEL_TYPE@ start position">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	291 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	292 </param>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	293 <param name="stop" type="text" label="@LABEL_TYPE@ end position">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	294 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	295 </param>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	296 <yield />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	297 </repeat>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	298 </xml>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	299
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	300 <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	301 <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	302 </xml>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	303
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	304 <xml name="macro_restrict" token_type="region" token_label_type="Region" >
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	305 <conditional name="@TYPE@s">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	306 <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	307 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	308 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	309 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	310 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	311 <when value="__none__"/>
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	312 <when value="@TYPE@s">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	313 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	314 <yield />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	315 </when>
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	316 <when value="@TYPE@s_file">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	317 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	318 <yield />
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	319 </when>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	320 </conditional>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	321 </xml>
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	322
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	323 <token name="@PARSE_INTERVALS@">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	324 <![CDATA[
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	325 #set $components = []
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	326 #for $i in $intervals:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	327 #set $chrom = str($i.chrom).strip()
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	328 #set $start = str($i.start).strip()
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	329 #set $stop = str($i.stop).strip()
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	330 #if $start or $stop:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	331 $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	332 #else:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	333 $components.append($chrom)
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	334 #end if
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	335 #end for
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	336 #set $intervals_spec = ','.join($components)
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	337 ]]>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	338 </token>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	339
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	340 <token name="@REGIONS@">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	341 <![CDATA[
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	342 #if $section.regions.regions_src == 'regions':
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	343 #set $intervals = $section.regions.regions
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	344 @PARSE_INTERVALS@
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	345 --regions '$intervals_spec'
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	346 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	347 #if $regions_path is not None:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	348 --regions-file '$regions_path'
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	349 #else:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	350 --regions-file '$section.regions.regions_file'
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	351 #end if
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	352 #end if
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	353 ]]>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	354 </token>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	355
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	356 <token name="@TARGETS@">
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	357 <![CDATA[
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	358 #if $targets_path:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	359 --targets-file "${section.targets.invert_targets_file}${targets_path}"
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	360 #elif $section.targets.targets_src == 'targets':
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	361 #set $intervals = $section.targets.targets
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	362 @PARSE_INTERVALS@
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	363 --targets '${section.targets.invert_targets_file}$intervals_spec'
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	364 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	365 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	366 #end if
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	367 ]]>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	368 </token>
611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	369
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	370 <token name="@PREPARE_REGIONS_FILE@">
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	371 <![CDATA[
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	372 #set $regions_path = None
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	373 #if 'regions' in $section
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	374 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	375 #if $section.regions.regions_file.ext.startswith('bed'):
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	376 #set $regions_path = 'regions_file.bed'
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	377 ln -s '$section.regions.regions_file' $regions_path &&
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	378 #end if
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	379 #end if
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	380 #end if
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	381 ]]>
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	382 </token>
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	383
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	384 <token name="@PREPARE_TARGETS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	385 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	386 #set $targets_path = None
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	387 #if 'targets' in $section
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	388 #if $section.targets.targets_src == 'targets_file':
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	389 #set $targets_path = 'targets_file.tab.gz'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	390 bgzip -c "$section.targets.targets_file" > $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	391 tabix -s 1 -b 2 -e 2 $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	392 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	393 #elif $tgts_sec.targets_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	394 #set $targets_path = 'targets_file.tab.gz'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	395 bgzip -c "$section.targets_file" > $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	396 tabix -s 1 -b 2 -e 2 $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	397 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	398 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	399 </token>
8 611f4cab1289 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	400
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	401 <token name="@TARGETS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	402 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	403 #if $targets_path is not None:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	404 --targets-file "${section.invert_targets_file}${targets_path}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	405 #elif $section.targets_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	406 --targets-file "${section.invert_targets_file}${section.targets_file}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	407 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	408 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	409 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	410
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	411 <xml name="macro_samples">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	412 <param argument="--samples" type="text" value="" optional="true" label="Samples"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	413 help="Comma separated list of samples to annotate (or exclude)">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	414 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	415 </param>
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	416 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	417 help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	418 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	419 help="File of samples to include" />
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	420 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	421 help="inverts the query/filtering applied by Samples file" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	422 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	423 <token name="@SAMPLES@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	424 #set $samples_defined = False
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	425 #if str($section.samples) != '':
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	426 #set $samples_defined = True
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	427 --samples '${section.invert_samples}${section.samples}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	428 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	429 #if $section.samples_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	430 #set $samples_defined = True
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	431 --samples-file "${section.invert_samples_file}${section.samples_file}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	432 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	433 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	434
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	435 <xml name="macro_sample">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	436 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	437 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	438 <token name="@SAMPLE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	439 #if $section.sample:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	440 --sample '${section.sample}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	441 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	442 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	443
12 02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	444 <xml name="macro_include_exclude_validate_sanitize">
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	445 <validator type="expression" message="Single quote or trailing backslash not allowed">"'" not in value and value[-1] != "\\"</validator>
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	446 <sanitizer>
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	447 <valid initial="string.ascii_letters,string.digits,string.whitespace,string.punctuation">
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	448 <remove value="@" />
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	449 <remove value="'" />
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	450 </valid>
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	451 </sanitizer>
02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	452 </xml>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	453
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	454 <xml name="macro_include">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	455 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
12 02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	456 <expand macro="macro_include_exclude_validate_sanitize" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	457 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	458 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	459 <token name="@INCLUDE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	460 #if $section.include:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	461 --include '${section.include}'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	462 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	463 </token>
12 02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	464
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	465 <xml name="macro_exclude">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	466 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
12 02f349bdbf96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3" iuc parents: 11 diff changeset	467 <expand macro="macro_include_exclude_validate_sanitize" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	468 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	469 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	470 <token name="@EXCLUDE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	471 #if $section.exclude:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	472 --exclude '${section.exclude}'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	473 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	474 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	475
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	476 <xml name="macro_columns">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	477 <param name="columns" type="text" value="" optional="true" label="Columns"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	478 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	479 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	480 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	481 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	482 <token name="@COLUMNS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	483 #if $section.columns != '':
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	484 --columns '${section.columns}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	485 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	486 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	487
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	488 <xml name="macro_haploid2diploid">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	489 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	490 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	491
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	492 <xml name="macro_vcf_ids">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	493 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	494 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	495 <token name="@VCF_IDS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	496 ${section.vcf_ids}
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	497 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	498
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	499 <token name="@OUTPUT_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	500 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	501 Output Type
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	502 -----------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	503
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	504 Output compressed BCF (b), or uncompressed VCF (v).
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	505 Use the BCF option when piping between bcftools subcommands to speed up
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	506 performance by removing unecessary compression/decompression
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	507 and VCF<->BCF conversion.
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	508
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	509 This Galaxy tool recommends using the compressed BCF format
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	510 as piping is not implemented, and uncompressed data would
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	511 use unnecessary amounts of space.
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	512 ]]></token>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	513 <token name="@REGIONS_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	514 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	515 Region Selections
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	516 -----------------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	517
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	518 Regions can be specified in a VCF,
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	519 BED, or tab-delimited file (the default). The columns of the
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	520 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	521 where positions are 1-based and inclusive. Uncompressed
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	522 files are stored in memory, while bgzip-compressed and
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	523 tabix-indexed region files are streamed. Note that sequence
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	524 names must match exactly, "chr20" is not the same as "20".
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	525 Also note that chromosome ordering in FILE will be
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	526 respected, the VCF will be processed in the order in which
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	527 chromosomes first appear in FILE. However, within
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	528 chromosomes, the VCF will always be processed in ascending
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	529 genomic coordinate order no matter what order they appear in
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	530 FILE. Note that overlapping regions in FILE can result in
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	531 duplicated out of order positions in the output. This option
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	532 requires indexed VCF/BCF files.
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	533 ]]></token>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	534 <token name="@TARGETS_HELP@"><![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	535 Targets
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	536 -------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	537
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	538 Similar to regions, but the next position is accessed by streaming the whole
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	539 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	540 applied simultaneously: regions uses the index to jump to a region and targets discards
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	541 positions which are not in the targets. Unlike regions, targets can be prefixed with
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	542 "^" to request logical complement. For example, "^X,Y,MT" indicates that
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	543 sequences X, Y and MT should be skipped. Yet another difference between the two
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	544 is that regions checks both start and end positions of indels, whereas targets checks
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	545 start positions only.
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	546
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	547 For the bcftools call command, with the option -C alleles, third column of the
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	548 targets file must be comma-separated list of alleles, starting with the
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	549 reference allele. Note that the file must be compressed and index. Such a file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	550 can be easily created from a VCF using::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	551
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	552 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf \| bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	553 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	554 <!-- TODO: galaxy-ify -->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	555 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	556
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	557
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	558 <token name="@COLLAPSE_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	559 Collapse
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	560 --------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	561
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	562 Controls how to treat records with duplicate positions and defines compatible
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	563 records across multiple input files. Here by "compatible" we mean records which
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	564 should be considered as identical by the tools. For example, when performing
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	565 line intersections, the desire may be to consider as identical all sites with
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	566 matching positions (bcftools isec -c all), or only sites with matching variant
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	567 type (bcftools isec -c snps -c indels), or only sites with all alleles
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	568 identical (bcftools isec -c none).
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	569
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	570
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	571 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	572 \| Flag value \| Result \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	573 +============+================================================================+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	574 \| none \| only records with identical REF and ALT alleles are compatible \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	575 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	576 \| some \| only records where some subset of ALT alleles match are \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	577 \| \| compatible \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	578 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	579 \| all \| all records are compatible, regardless of whether the ALT \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	580 \| \| alleles match or not. In the case of records with the same \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	581 \| \| position, only the first wil lbe considered and appear on \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	582 \| \| output. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	583 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	584 \| snps \| any SNP records are compatible, regardless of whether the ALT \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	585 \| \| alleles match or not. For duplicate positions, only the first \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	586 \| \| SNP record will be considered and appear on output. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	587 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	588 \| indels \| all indel records are compatible, regardless of whether the \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	589 \| \| REF and ALT alleles match or not. For duplicate positions, \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	590 \| \| only the first indel record will be considered and appear on \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	591 \| \| output. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	592 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	593 \| both \| abbreviation of "-c indels -c snps" \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	594 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	595 \| id \| only records with identical ID column are compatible. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	596 \| \| Supportedby bcftools merge only. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	597 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	598 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	599
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	600 <token name="@EXPRESSIONS_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	601 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	602 Expressions
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	603 -----------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	604
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	605 Valid expressions may contain:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	606
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	607 - numerical constants, string constants
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	608
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	609 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	610
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	611 1, 1.0, 1e-4
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	612 "String"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	613
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	614 - arithmetic operators
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	615
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	616 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	617
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	618 +,*,-,/
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	619
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	620 - comparison operators
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	621
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	622 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	623
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	624 == (same as =), >, >=, <=, <, !=
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	625
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	626 - regex operators "~" and its negation "!~"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	627
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	628 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	629
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	630 INFO/HAYSTACK ~ "needle"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	631
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	632 - parentheses
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	633
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	634 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	635
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	636 (, )
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	637
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	638 - logical operators
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	639
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	640 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	641
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	642 && (same as &), \|\|, \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	643
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	644 - INFO tags, FORMAT tags, column names
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	645
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	646 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	647
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	648 INFO/DP or DP
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	649 FORMAT/DV, FMT/DV, or DV
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	650 FILTER, QUAL, ID, REF, ALT[0]
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	651
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	652 - 1 (or 0) to test the presence (or absence) of a flag
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	653
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	654 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	655
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	656 FlagA=1 && FlagB=0
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	657
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	658 - "." to test missing values
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	659
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	660 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	661
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	662 DP=".", DP!=".", ALT="."
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	663
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	664 - missing genotypes can be matched regardless of phase and ploidy (".\|.", "./.", ".") using this expression
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	665
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	666 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	667
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	668 GT="."
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	669
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	670 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	671
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	672 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	673
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	674 TYPE="indel" \| TYPE="snp"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	675
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	676 - array subscripts, "*" for any field
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	677
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	678 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	679
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	680 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	681 DP4[*] == 0
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	682 CSQ[] ~ "missense_variant.deleterious"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	683
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	684 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	685
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	686 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	687
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	688 MAX, MIN, AVG, SUM, STRLEN, ABS
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	689
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	690 - variables calculated on the fly if not present: number of alternate alleles; number of samples; count of alternate alleles; minor allele count (similar to AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	691
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	692 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	693
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	694 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	695
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	696 Notes:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	697
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	698 - String comparisons and regular expressions are case-insensitive
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	699 - If the subscript "*" is used in regular expression search, the whole field
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	700 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	701 true for the string vector INFO/STR=AB,CD.
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	702 - Variables and function names are case-insensitive, but not tag names. For
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	703 example, "qual" can be used instead of "QUAL", "strlen()" instead of
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	704 "STRLEN()" , but not "dp" instead of "DP".
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	705
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	706 Examples:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	707
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	708 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	709
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	710 MIN(DV)>5
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	711 MIN(DV/DP)>0.3
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	712 MIN(DP)>10 & MIN(DV)>3
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	713 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	714 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	715 QUAL>10 \| FMT/GQ>10 .. selects only GQ>10 samples
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	716 QUAL>10 \|\| FMT/GQ>10 .. selects all samples at QUAL>10 sites
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	717 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	718 MIN(DP)>35 && AVG(GQ)>50
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	719 ID=@file .. selects lines with ID present in the file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	720 ID!=@~/file .. skip lines with ID present in the ~/file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	721 MAF[0]<0.05 .. select rare variants at 5% cutoff
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	722 ]]></token>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	723 </macros>

Mercurial > repos > iuc > bcftools_isec

annotate macros.xml @ 15:97d19c008d15 draft