bcftools_merge: macros.xml annotate

annotate macros.xml @ 8:beb87637bee3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

author	iuc
date	Wed, 05 Jun 2019 13:01:16 -0400
parents	7ba36babba2d
children	27026ed52654

rev	line source
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	1 <macros>
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	2 <token name="@TOOL_VERSION@">1.9</token>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	3 <xml name="requirements">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	4 <requirements>
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	5 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	6 <requirement type="package" version="1.9">htslib</requirement>
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	7 <yield />
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	8 </requirements>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	9 </xml>
5 c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	10 <xml name="samtools_requirement">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	11 <requirement type="package" version="1.9">samtools</requirement>
5 c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	12 </xml>
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	13 <xml name="matplotlib_requirement">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	14 <requirement type="package" version="3.1.0">matplotlib</requirement>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	15 </xml>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	16 <xml name="version_command">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	17 <version_command>bcftools 2>&1 \| grep 'Version:'</version_command>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	18 </xml>
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	19
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	20 <xml name="citations">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	21 <citations>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	22 <citation type="doi">10.1093/bioinformatics/btp352</citation>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	23 <yield />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	24 </citations>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	25 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	26 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	27 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	28 <token name="@THREADS@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	29 --threads \${GALAXY_SLOTS:-4}
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	30 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	31 <token name="@PREPARE_ENV@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	32 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	33 export BCFTOOLS_PLUGINS=`which bcftools \| sed 's,bin/bcftools,libexec/bcftools,'`;
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	34 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	35 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	36 <xml name="macro_input">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	37 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	38 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	39 <token name="@PREPARE_INPUT_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	40 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	41 ## May need to symlink input if there is an associated
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	42 #set $input_vcf = 'input.vcf.gz'
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	43 #if $input_file.is_of_type('vcf')
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	44 bgzip -c '$input_file' > $input_vcf &&
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	45 bcftools index $input_vcf &&
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	46 #elif $input_file.is_of_type('vcf_bgzip')
6 85ee7e6c4204 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3 iuc parents: 5 diff changeset	47 ln -s '$input_file' $input_vcf &&
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	48 #if $input_file.metadata.tabix_index:
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	49 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	50 #else
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	51 bcftools index $input_vcf &&
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	52 #end if
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	53 #elif $input_file.is_of_type('bcf')
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	54 #set $input_vcf = 'input.bcf'
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	55 ln -s '$input_file' $input_vcf &&
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	56 #if $input_file.metadata.bcf_index:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	57 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	58 #else
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	59 bcftools index $input_vcf &&
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	60 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	61 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	62 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	63 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	64 <token name="@INPUT_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	65 $input_vcf
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	66 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	67
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	68 <xml name="macro_inputs">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	69 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	70 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	71 <token name="@PREPARE_INPUT_FILES@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	72 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	73 ## May need to symlink input if there is an associated
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	74 #set $input_vcfs = []
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	75 #set $vcfs_list_file = 'vcfs_list'
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	76 #for (i, input_file) in enumerate($input_files):
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	77 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	78 #if $input_file.is_of_type('vcf')
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	79 bgzip -c '$input_file' > $input_vcf &&
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	80 bcftools index $input_vcf &&
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	81 #elif $input_file.is_of_type('vcf_bgzip')
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	82 ln -s '$input_file' $input_vcf &&
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	83 #if $input_file.metadata.tabix_index:
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	84 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	85 #else
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	86 bcftools index $input_vcf &&
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	87 #end if
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	88 #elif $input_file.is_of_type('bcf')
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	89 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	90 ln -s '$input_file' $input_vcf &&
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	91 #if $input_file.metadata.bcf_index:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	92 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	93 #else
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	94 bcftools index $input_vcf &&
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	95 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	96 #end if
1 e8eceb3a69a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06 iuc parents: 0 diff changeset	97 echo '$input_vcf' >> $vcfs_list_file &&
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	98 $input_vcfs.append($input_vcf)
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	99 #end for
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	100 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	101 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	102 <token name="@INPUT_FILES@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	103 #echo ' '.join($input_vcfs)#
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	104 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	105 <token name="@INPUT_LIST_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	106 $vcfs_list_file
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	107 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	108
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	109 <xml name="test_using_reference" token_select_from="history" token_ref="">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	110 <conditional name="reference_source">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	111 <param name="reference_source_selector" value="@SELECT_FROM@" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	112 <param name="fasta_ref" ftype="fasta" value="@REF@" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	113 </conditional>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	114 </xml>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	115
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	116 <xml name="macro_fasta_ref">
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	117 <conditional name="reference_source">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	118 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	119 <option value="cached">Use a built-in genome</option>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	120 <option value="history">Use a genome from the history</option>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	121 </param>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	122 <when value="cached">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	123 <param name="fasta_ref" type="select" label="Reference genome">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	124 <options from_data_table="fasta_indexes">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	125 <filter type="data_meta" column="1" key="dbkey" ref="input_file" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	126 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	127 </options>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	128 </param>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	129 </when>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	130 <when value="history">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	131 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	132 </when>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	133 </conditional>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	134 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	135 <token name="@PREPARE_FASTA_REF@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	136 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	137 #set $input_fa_ref = None
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	138 #if 'fasta_ref' in $section and $section.fasta_ref:
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	139 #if 'reference_source_selector' in $section:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	140 #if str($section.reference_source_selector) == "history":
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	141 #set $input_fa_ref = 'ref.fa'
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	142 ln -s '$section.fasta_ref' $input_fa_ref &&
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	143 samtools faidx $input_fa_ref &&
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	144 #else:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	145 #set $input_fa_ref = str($section.fasta_ref.fields.path)
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	146 #end if
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	147 #end if
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	148 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	149 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	150 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	151 <token name="@FASTA_REF@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	152 #if $input_fa_ref is not None:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	153 --fasta-ref $input_fa_ref
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	154 #elif 'fasta_ref' in $section and $section.fasta_ref:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	155 --fasta-ref '${section.fasta_ref}'
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	156 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	157 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	158
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	159 <xml name="macro_AF_file">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	160 <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 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	161 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	162 <!-- This may need to bgzip and tabix the file -->
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	163 <token name="@PREPARE_AF_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	164 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	165 #if 'AF_file' in $section and $section.AF_file:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	166 #pass
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	167 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	168 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	169 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	170 <token name="@AF_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	171 #if 'AF_file' in $section and $section.AF_file:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	172 --AF-file '${section.AF_file}'
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	173 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	174 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	175
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	176 <xml name="macro_estimate_AF">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	177 <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 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	178 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	179 <token name="@ESTIMATE_AF@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	180 #if 'estimate_AF' in $section and $section.estimate_AF:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	181 --estimate-AF "${section.estimate_AF}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	182 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	183 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	184
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	185 <xml name="macro_exons_file">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	186 <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 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	187 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	188 <token name="@PREPARE_EXONS_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	189 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	190 #set $exons_path = None
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	191 #if 'exons_file' in $section and $section.exons_file:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	192 #set $exons_path = 'exons_file.tab.gz'
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	193 bgzip -c "$section.exons_file" > $exons_path &&
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	194 tabix -s 1 -b 2 -e 3 $exons_path &&
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	195 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	196 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	197 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	198 <token name="@EXONS_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	199 #if 'exons_file' in $section and $section.exons_file:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	200 --exons $exons_path
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	201 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	202 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	203
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	204 <xml name="macro_ploidy_file">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	205 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	206 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	207 <token name="@PLOIDY_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	208 #if 'ploidy_file' in $section and $section.ploidy_file:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	209 --ploidy "${section.ploidy_file}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	210 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	211 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	212
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	213 <xml name="macro_collapse_opt_none">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	214 <option value="none">none - require the exact same set of alleles in all files</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	215 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	216 <xml name="macro_collapse_opt_id">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	217 <option value="id">id - only records with identical ID column are compatible. </option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	218 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	219 <xml name="macro_collapse">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	220 <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 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	221 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	222 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	223 <option value="both">both - indels and snps </option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	224 <option value="some">some - at least some of the ALTs must match</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	225 <option value="any">any - any combination of alleles</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	226 <yield/>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	227 </param>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	228 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	229 <token name="@COLLAPSE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	230 #if $section.collapse:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	231 --collapse ${section.collapse}
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	232 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	233 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	234
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	235 <xml name="macro_apply_filters">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	236 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	237 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")">
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	238 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	239 </param>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	240 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	241 <token name="@APPLY_FILTERS@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	242 #if $section.apply_filters:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	243 --apply-filters '${section.apply_filters}'
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	244 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	245 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	246
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	247 <xml name="macro_select_output_type">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	248 <param name="output_type" type="select">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	249 <option value="b">compressed BCF</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	250 <!-- no galaxy datatypes for these
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	251 <option value="u">uncompressed BCF</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	252 <option value="z">compressed VCF</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	253 -->
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	254 <option value="v">uncompressed VCF</option>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	255 </param>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	256 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	257 <token name="@OUTPUT_TYPE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	258 #if str($output_type) != "__none__":
5 c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	259 --output-type '${output_type}'
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	260 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	261 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	262
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	263 <xml name="macro_vcf_output">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	264 <data name="output_file" format="vcf">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	265 <change_format>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	266 <when input="output_type" value="b" format="bcf" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	267 <when input="output_type" value="u" format="bcf" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	268 <when input="output_type" value="z" format="vcf_bgzip" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	269 <when input="output_type" value="v" format="vcf" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	270 </change_format>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	271 </data>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	272 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	273
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	274 <xml name="macro_invert_targets">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	275 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue=""
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	276 label="Invert Targets"
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	277 help="inverts the query/filtering applied by the targets" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	278 </xml>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	279
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	280 <xml name="macro_restriction_spec" token_type="region" token_label_type="Region">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	281 <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	282 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	283 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	284 </param>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	285 <param name="start" type="text" label="@LABEL_TYPE@ start position">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	286 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	287 </param>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	288 <param name="stop" type="text" label="@LABEL_TYPE@ end position">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	289 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	290 </param>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	291 <yield />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	292 </repeat>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	293 </xml>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	294
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	295 <xml name="macro_restrictions_file" token_type="region" token_label_type="Region">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	296 <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	297 </xml>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	298
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	299 <xml name="macro_restrict" token_type="region" token_label_type="Region" >
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	300 <conditional name="@TYPE@s">
beb87637bee3 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_src" type="select" label="@LABEL_TYPE@s">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	302 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	303 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	304 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	305 </param>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	306 <when value="__none__"/>
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	307 <when value="@TYPE@s">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	308 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	309 <yield />
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	310 </when>
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	311 <when value="@TYPE@s_file">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	312 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	313 <yield />
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	314 </when>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	315 </conditional>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	316 </xml>
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	317
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	318 <token name="@PARSE_INTERVALS@">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	319 <![CDATA[
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	320 #set $components = []
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	321 #for $i in $intervals:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	322 #set $chrom = str($i.chrom).strip()
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	323 #set $start = str($i.start).strip()
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	324 #set $stop = str($i.stop).strip()
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	325 #if $start or $stop:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	326 $components.append($chrom + ':' + ($start or '0') + '-' + $stop)
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	327 #else:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	328 $components.append($chrom)
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	329 #end if
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	330 #end for
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	331 #set $intervals_spec = ','.join($components)
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	332 ]]>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	333 </token>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	334
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	335 <token name="@REGIONS@">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	336 <![CDATA[
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	337 #if $section.regions.regions_src == 'regions':
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	338 #set $intervals = $section.regions.regions
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	339 @PARSE_INTERVALS@
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	340 --regions '$intervals_spec'
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	341 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	342 #if $regions_path is not None:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	343 --regions-file '$regions_path'
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	344 #else:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	345 --regions-file '$section.regions.regions_file'
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	346 #end if
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	347 #end if
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	348 ]]>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	349 </token>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	350
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	351 <token name="@TARGETS@">
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	352 <![CDATA[
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	353 #if $targets_path:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	354 --targets-file "${section.targets.invert_targets_file}${targets_path}"
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	355 #elif $section.targets.targets_src == 'targets':
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	356 #set $intervals = $section.targets.targets
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	357 @PARSE_INTERVALS@
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	358 --targets '${section.targets.invert_targets_file}$intervals_spec'
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	359 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	360 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	361 #end if
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	362 ]]>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	363 </token>
beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	364
5 c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	365 <token name="@PREPARE_REGIONS_FILE@">
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	366 <![CDATA[
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	367 #set $regions_path = None
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	368 #if 'regions' in $section
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	369 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	370 #if $section.regions.regions_file.ext.startswith('bed'):
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	371 #set $regions_path = 'regions_file.bed'
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	372 ln -s '$section.regions.regions_file' $regions_path &&
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	373 #end if
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	374 #end if
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	375 #end if
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	376 ]]>
c5c61f2f8757 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	377 </token>
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	378
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	379 <token name="@PREPARE_TARGETS_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	380 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	381 #set $targets_path = None
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	382 #if 'targets' in $section
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	383 #if $section.targets.targets_src == 'targets_file':
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	384 #set $targets_path = 'targets_file.tab.gz'
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	385 bgzip -c "$section.targets.targets_file" > $targets_path &&
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	386 tabix -s 1 -b 2 -e 2 $targets_path &&
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	387 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	388 #elif $tgts_sec.targets_file:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	389 #set $targets_path = 'targets_file.tab.gz'
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	390 bgzip -c "$section.targets_file" > $targets_path &&
5add48c63b9a 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 &&
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	392 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	393 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	394 </token>
8 beb87637bee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5 iuc parents: 7 diff changeset	395
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	396 <token name="@TARGETS_FILE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	397 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	398 #if $targets_path is not None:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	399 --targets-file "${section.invert_targets_file}${targets_path}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	400 #elif $section.targets_file:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	401 --targets-file "${section.invert_targets_file}${section.targets_file}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	402 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	403 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	404 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	405
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	406 <xml name="macro_samples">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	407 <param argument="--samples" type="text" value="" optional="true" label="Samples"
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	408 help="Comma separated list of samples to annotate (or exclude)">
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	409 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	410 </param>
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	411 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	412 help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	413 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	414 help="File of samples to include" />
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	415 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	416 help="inverts the query/filtering applied by Samples file" />
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	417 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	418 <token name="@SAMPLES@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	419 #set $samples_defined = False
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	420 #if str($section.samples) != '':
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	421 #set $samples_defined = True
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	422 --samples '${section.invert_samples}${section.samples}'
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	423 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	424 #if $section.samples_file:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	425 #set $samples_defined = True
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	426 --samples-file "${section.invert_samples_file}${section.samples_file}"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	427 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	428 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	429
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	430 <xml name="macro_sample">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	431 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	432 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	433 <token name="@SAMPLE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	434 #if $section.sample:
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	435 --sample '${section.sample}'
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	436 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	437 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	438
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	439
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	440 <xml name="macro_include">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	441 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	442 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	443 <sanitizer sanitize="False"/>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	444 </param>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	445 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	446 <token name="@INCLUDE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	447 #if $section.include:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	448 --include '${section.include}'
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	449 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	450 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	451
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	452 <xml name="macro_exclude">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	453 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	454 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	455 <sanitizer sanitize="False"/>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	456 </param>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	457 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	458 <token name="@EXCLUDE@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	459 #if $section.exclude:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	460 --exclude '${section.exclude}'
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	461 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	462 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	463
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	464 <xml name="macro_columns">
7 7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	465 <param name="columns" type="text" value="" optional="true" label="Columns"
7ba36babba2d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	466 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	467 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	468 </param>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	469 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	470 <token name="@COLUMNS@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	471 #if $section.columns != '':
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	472 --columns '${section.columns}'
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	473 #end if
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	474 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	475
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	476 <xml name="macro_haploid2diploid">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	477 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	478 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	479
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	480 <xml name="macro_vcf_ids">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	481 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	482 </xml>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	483 <token name="@VCF_IDS@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	484 ${section.vcf_ids}
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	485 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	486
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	487 <token name="@OUTPUT_HELP@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	488 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	489 Output Type
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	490 -----------
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	491
3 d6f351f2d6a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	492 Output compressed BCF (b), or uncompressed VCF (v).
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	493 Use the BCF option when piping between bcftools subcommands to speed up
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	494 performance by removing unecessary compression/decompression
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	495 and VCF<->BCF conversion.
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	496
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	497 This Galaxy tool recommends using the compressed BCF format
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	498 as piping is not implemented, and uncompressed data would
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	499 use unnecessary amounts of space.
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	500 ]]></token>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	501 <token name="@REGIONS_HELP@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	502 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	503 Region Selections
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	504 -----------------
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	505
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	506 Regions can be specified in a VCF,
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	507 BED, or tab-delimited file (the default). The columns of the
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	508 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	509 where positions are 1-based and inclusive. Uncompressed
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	510 files are stored in memory, while bgzip-compressed and
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	511 tabix-indexed region files are streamed. Note that sequence
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	512 names must match exactly, "chr20" is not the same as "20".
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	513 Also note that chromosome ordering in FILE will be
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	514 respected, the VCF will be processed in the order in which
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	515 chromosomes first appear in FILE. However, within
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	516 chromosomes, the VCF will always be processed in ascending
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	517 genomic coordinate order no matter what order they appear in
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	518 FILE. Note that overlapping regions in FILE can result in
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	519 duplicated out of order positions in the output. This option
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	520 requires indexed VCF/BCF files.
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	521 ]]></token>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	522 <token name="@TARGETS_HELP@"><![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	523 Targets
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	524 -------
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	525
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	526 Similar to regions, but the next position is accessed by streaming the whole
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	527 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	528 applied simultaneously: regions uses the index to jump to a region and targets discards
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	529 positions which are not in the targets. Unlike regions, targets can be prefixed with
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	530 "^" to request logical complement. For example, "^X,Y,MT" indicates that
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	531 sequences X, Y and MT should be skipped. Yet another difference between the two
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	532 is that regions checks both start and end positions of indels, whereas targets checks
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	533 start positions only.
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	534
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	535 For the bcftools call command, with the option -C alleles, third column of the
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	536 targets file must be comma-separated list of alleles, starting with the
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	537 reference allele. Note that the file must be compressed and index. Such a file
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	538 can be easily created from a VCF using::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	539
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	540 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf \| bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	541 ]]>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	542 <!-- TODO: galaxy-ify -->
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	543 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	544
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	545
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	546 <token name="@COLLAPSE_HELP@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	547 Collapse
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	548 --------
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	549
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	550 Controls how to treat records with duplicate positions and defines compatible
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	551 records across multiple input files. Here by "compatible" we mean records which
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	552 should be considered as identical by the tools. For example, when performing
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	553 line intersections, the desire may be to consider as identical all sites with
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	554 matching positions (bcftools isec -c all), or only sites with matching variant
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	555 type (bcftools isec -c snps -c indels), or only sites with all alleles
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	556 identical (bcftools isec -c none).
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	557
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	558
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	559 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	560 \| Flag value \| Result \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	561 +============+================================================================+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	562 \| none \| only records with identical REF and ALT alleles are compatible \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	563 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	564 \| some \| only records where some subset of ALT alleles match are \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	565 \| \| compatible \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	566 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	567 \| all \| all records are compatible, regardless of whether the ALT \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	568 \| \| alleles match or not. In the case of records with the same \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	569 \| \| position, only the first wil lbe considered and appear on \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	570 \| \| output. \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	571 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	572 \| snps \| any SNP records are compatible, regardless of whether the ALT \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	573 \| \| alleles match or not. For duplicate positions, only the first \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	574 \| \| SNP record will be considered and appear on output. \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	575 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	576 \| indels \| all indel records are compatible, regardless of whether the \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	577 \| \| REF and ALT alleles match or not. For duplicate positions, \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	578 \| \| only the first indel record will be considered and appear on \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	579 \| \| output. \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	580 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	581 \| both \| abbreviation of "-c indels -c snps" \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	582 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	583 \| id \| only records with identical ID column are compatible. \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	584 \| \| Supportedby bcftools merge only. \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	585 +------------+----------------------------------------------------------------+
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	586 </token>
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	587
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	588 <token name="@EXPRESSIONS_HELP@">
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	589 <![CDATA[
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	590 Expressions
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	591 -----------
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	592
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	593 Valid expressions may contain:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	594
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	595 - numerical constants, string constants
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	596
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	597 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	598
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	599 1, 1.0, 1e-4
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	600 "String"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	601
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	602 - arithmetic operators
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	603
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	604 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	605
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	606 +,*,-,/
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	607
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	608 - comparison operators
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	609
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	610 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	611
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	612 == (same as =), >, >=, <=, <, !=
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	613
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	614 - regex operators "~" and its negation "!~"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	615
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	616 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	617
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	618 INFO/HAYSTACK ~ "needle"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	619
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	620 - parentheses
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	621
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	622 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	623
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	624 (, )
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	625
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	626 - logical operators
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	627
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	628 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	629
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	630 && (same as &), \|\|, \|
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	631
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	632 - INFO tags, FORMAT tags, column names
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	633
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	634 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	635
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	636 INFO/DP or DP
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	637 FORMAT/DV, FMT/DV, or DV
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	638 FILTER, QUAL, ID, REF, ALT[0]
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	639
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	640 - 1 (or 0) to test the presence (or absence) of a flag
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	641
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	642 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	643
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	644 FlagA=1 && FlagB=0
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	645
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	646 - "." to test missing values
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	647
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	648 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	649
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	650 DP=".", DP!=".", ALT="."
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	651
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	652 - missing genotypes can be matched regardless of phase and ploidy (".\|.", "./.", ".") using this expression
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	653
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	654 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	655
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	656 GT="."
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	657
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	658 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	659
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	660 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	661
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	662 TYPE="indel" \| TYPE="snp"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	663
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	664 - array subscripts, "*" for any field
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	665
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	666 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	667
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	668 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	669 DP4[*] == 0
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	670 CSQ[] ~ "missense_variant.deleterious"
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	671
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	672 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	673
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	674 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	675
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	676 MAX, MIN, AVG, SUM, STRLEN, ABS
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	677
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	678 - 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
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	679
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	680 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	681
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	682 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	683
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	684 Notes:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	685
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	686 - String comparisons and regular expressions are case-insensitive
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	687 - If the subscript "*" is used in regular expression search, the whole field
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	688 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	689 true for the string vector INFO/STR=AB,CD.
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	690 - Variables and function names are case-insensitive, but not tag names. For
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	691 example, "qual" can be used instead of "QUAL", "strlen()" instead of
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	692 "STRLEN()" , but not "dp" instead of "DP".
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	693
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	694 Examples:
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	695
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	696 ::
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	697
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	698 MIN(DV)>5
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	699 MIN(DV/DP)>0.3
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	700 MIN(DP)>10 & MIN(DV)>3
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	701 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	702 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	703 QUAL>10 \| FMT/GQ>10 .. selects only GQ>10 samples
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	704 QUAL>10 \|\| FMT/GQ>10 .. selects all samples at QUAL>10 sites
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	705 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	706 MIN(DP)>35 && AVG(GQ)>50
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	707 ID=@file .. selects lines with ID present in the file
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	708 ID!=@~/file .. skip lines with ID present in the ~/file
5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	709 MAF[0]<0.05 .. select rare variants at 5% cutoff
4 df40d7f9737c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	710 ]]></token>
0 5add48c63b9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	711 </macros>

Mercurial > repos > iuc > bcftools_merge

annotate macros.xml @ 8:beb87637bee3 draft