bcftools_isec: macros.xml annotate

annotate macros.xml @ 7:709dd8291b83 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69

author	iuc
date	Thu, 21 Feb 2019 16:06:03 -0500
parents	c803c34361e0
children	611f4cab1289

rev	line source
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	1 <macros>
7 709dd8291b83 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 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	3 <xml name="stdio">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	4 <stdio>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	5 <exit_code range="1:" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	6 <exit_code range=":-1" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	7 <regex match="Error:" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	8 <regex match="Exception:" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	9 </stdio>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	10 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	11 <xml name="requirements">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	12 <requirements>
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	13 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	14 <requirement type="package" version="1.9">htslib</requirement>
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	15 <yield />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	16 </requirements>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	17 </xml>
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	18 <xml name="samtools_requirement">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	19 <requirement type="package" version="1.9">samtools</requirement>
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	20 </xml>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	21 <xml name="version_command">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	22 <version_command>bcftools 2>&1 \| grep 'Version:'</version_command>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	23 </xml>
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	24
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	25 <xml name="citations">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	26 <citations>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	27 <citation type="doi">10.1093/bioinformatics/btp352</citation>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	28 <yield />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	29 </citations>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	30 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	31 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	32 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	33 <token name="@THREADS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	34 --threads \${GALAXY_SLOTS:-4}
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	35 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	36 <token name="@PREPARE_ENV@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	37 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	38 export BCFTOOLS_PLUGINS=`which bcftools \| sed 's,bin/bcftools,libexec/bcftools,'`;
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	39 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	40 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	41 <xml name="macro_input">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	43 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	44 <token name="@PREPARE_INPUT_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	45 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	46 ## May need to symlink input if there is an associated
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	47 #set $input_vcf = 'input.vcf.gz'
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	48 #if $input_file.is_of_type('vcf')
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	49 bgzip -c '$input_file' > $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	50 bcftools index $input_vcf &&
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	51 #elif $input_file.is_of_type('vcf_bgzip')
6 c803c34361e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3 iuc parents: 5 diff changeset	52 ln -s '$input_file' $input_vcf &&
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	53 #if $input_file.metadata.tabix_index:
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	54 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	55 #else
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	56 bcftools index $input_vcf &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	57 #end if
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	58 #elif $input_file.is_of_type('bcf')
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	59 #set $input_vcf = 'input.bcf'
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	60 ln -s '$input_file' $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	61 #if $input_file.metadata.bcf_index:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	62 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	63 #else
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	64 bcftools index $input_vcf &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	65 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	66 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	67 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	68 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	69 <token name="@INPUT_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	70 $input_vcf
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	71 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	72
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	73 <xml name="macro_inputs">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	74 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	75 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	76 <token name="@PREPARE_INPUT_FILES@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	77 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	78 ## May need to symlink input if there is an associated
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	79 #set $input_vcfs = []
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	80 #set $vcfs_list_file = 'vcfs_list'
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	81 #for (i, input_file) in enumerate($input_files):
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	82 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	83 #if $input_file.is_of_type('vcf')
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	84 bgzip -c '$input_file' > $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	85 bcftools index $input_vcf &&
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	86 #elif $input_file.is_of_type('vcf_bgzip')
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	87 ln -s '$input_file' $input_vcf &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	88 #if $input_file.metadata.tabix_index:
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	89 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	90 #else
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	91 bcftools index $input_vcf &&
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	92 #end if
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	93 #elif $input_file.is_of_type('bcf')
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	94 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	95 ln -s '$input_file' $input_vcf &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	96 #if $input_file.metadata.bcf_index:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	97 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	98 #else
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	99 bcftools index $input_vcf &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	100 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	101 #end if
1 ddf3dd241f7c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06 iuc parents: 0 diff changeset	102 echo '$input_vcf' >> $vcfs_list_file &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	103 $input_vcfs.append($input_vcf)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	104 #end for
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	105 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	106 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	107 <token name="@INPUT_FILES@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	108 #echo ' '.join($input_vcfs)#
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	109 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	110 <token name="@INPUT_LIST_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	111 $vcfs_list_file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	112 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	113
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	114 <xml name="macro_fasta_ref">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	115 <param name="fasta_ref" argument="--fasta-ref" type="data" format="data" optional="true" label="Reference sequence in FASTA format" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	116 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	117 <token name="@PREPARE_FASTA_REF@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	118 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	119 #set $input_fa_ref = None
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	120 #if 'fasta_ref' in $section and $section.fasta_ref:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	121 #set $input_fa_ref = 'ref.fa'
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	122 ln -s '$section.fasta_ref' $input_fa_ref &&
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	123 samtools faidx $input_fa_ref &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	124 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	125 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	126 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	127 <token name="@FASTA_REF@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	128 #if $input_fa_ref is not None:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	129 --fasta-ref $input_fa_ref
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	130 #elif 'fasta_ref' in $section and $section.fasta_ref:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	131 --fasta-ref '${section.fasta_ref}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	132 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	133 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	134
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	135 <xml name="macro_ref_fasta">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	136 <conditional name="reference_source">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	137 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	138 <option value="cached">Locally cached</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	139 <option value="history">History</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	140 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	141 <when value="cached">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	142 <param name="ref_file" type="select" label="Select reference genome">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	143 <options from_data_table="fasta_indexes">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	144 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	145 </options>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	146 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	147 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	148 </when>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	149 <when value="history"> <!-- FIX ME!!!! -->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	150 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	151 </when>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	152 </conditional>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	153 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	154
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	155
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	156 <xml name="macro_AF_file">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	157 <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	158 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	159 <!-- This may need to bgzip and tabix the file -->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	160 <token name="@PREPARE_AF_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	161 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	162 #if 'AF_file' in $section and $section.AF_file:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	163 #pass
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	164 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	165 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	166 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	167 <token name="@AF_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	168 #if 'AF_file' in $section and $section.AF_file:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	169 --AF-file '${section.AF_file}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	170 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	171 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	172
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	173 <xml name="macro_estimate_AF">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	174 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	175 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	176 <token name="@ESTIMATE_AF@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	177 #if 'estimate_AF' in $section and $section.estimate_AF:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	178 --estimate-AF "${section.estimate_AF}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	179 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	180 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	181
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	182 <xml name="macro_exons_file">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	183 <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	184 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	185 <token name="@PREPARE_EXONS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	186 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	187 #set $exons_path = None
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	188 #if 'exons_file' in $section and $section.exons_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	189 #set $exons_path = 'exons_file.tab.gz'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	190 bgzip -c "$section.exons_file" > $exons_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	191 tabix -s 1 -b 2 -e 3 $exons_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	192 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	193 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	194 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	195 <token name="@EXONS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	196 #if 'exons_file' in $section and $section.exons_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	197 --exons $exons_path
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	198 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	199 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	200
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	201 <xml name="macro_ploidy_file">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	202 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	203 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	204 <token name="@PLOIDY_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	205 #if 'ploidy_file' in $section and $section.ploidy_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	206 --ploidy "${section.ploidy_file}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	207 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	208 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	209
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	210 <xml name="macro_collapse_opt_none">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	211 <option value="none">none - require the exact same set of alleles in all files</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	212 </xml>
a994b57c9a7d 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_id">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	214 <option value="id">id - only records with identical ID column are compatible. </option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	215 </xml>
a994b57c9a7d 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">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	217 <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	218 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	219 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	220 <option value="both">both - indels and snps </option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	221 <option value="some">some - at least some of the ALTs must match</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	222 <option value="any">any - any combination of alleles</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	223 <yield/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	224 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	225 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	226 <token name="@COLLAPSE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	227 #if $section.collapse:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	228 --collapse ${section.collapse}
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	229 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	230 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	231
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	232 <xml name="macro_apply_filters">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	233 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	234 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	235 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	236 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	237 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	238 <token name="@APPLY_FILTERS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	239 #if $section.apply_filters:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	240 --apply-filters '${section.apply_filters}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	241 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	242 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	243
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	244 <xml name="macro_select_output_type">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	245 <param name="output_type" type="select">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	246 <option value="b">compressed BCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	247 <!-- no galaxy datatypes for these
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	248 <option value="u">uncompressed BCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	249 <option value="z">compressed VCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	250 -->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	251 <option value="v">uncompressed VCF</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	252 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	253 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	254 <token name="@OUTPUT_TYPE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	255 #if str($output_type) != "__none__":
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	256 --output-type '${output_type}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	257 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	258 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	259
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	260 <xml name="macro_vcf_output">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	261 <data name="output_file" format="vcf">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	262 <change_format>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	263 <when input="output_type" value="b" format="bcf" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	264 <when input="output_type" value="u" format="bcf" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	265 <when input="output_type" value="z" format="vcf_bgzip" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	266 <when input="output_type" value="v" format="vcf" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	267 </change_format>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	268 </data>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	269 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	270
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	271 <xml name="macro_regions">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	272 <conditional name="regions">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	273 <param name="regions_src" type="select" label="Regions">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	274 <option value="__none__">None</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	275 <option value="regions">regions</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	276 <option value="regions_file">regions-file</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	277 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	278 <when value="__none__"/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	279 <when value="regions">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	280 <param name="regions" type="text" value="" optional="true" label="Restrict to comma-separated list of regions"
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	281 help="Each region is specifed as: chr or chr:pos or chr:from-to">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	282 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	283 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	284 </when>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	285 <when value="regions_file">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	286 <param name="regions_file" type="data" format="vcf,bed,tabular" optional="true" label="Regions file" help="Restrict to regions listed in a file" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	287 </when>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	288 </conditional>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	289 </xml>
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	290 <token name="@PREPARE_REGIONS_FILE@">
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	291 <![CDATA[
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	292 #set $regions_path = None
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	293 #if 'regions' in $section
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	294 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	295 #if $section.regions.regions_file.ext.startswith('bed'):
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	296 #set $regions_path = 'regions_file.bed'
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	297 ln -s '$section.regions.regions_file' $regions_path &&
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	298 #end if
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	299 #end if
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	300 #end if
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	301 ]]>
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	302 </token>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	303 <token name="@REGIONS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	304 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	305 --regions '$section.regions.regions'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	306 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
5 cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	307 #if $regions_path is not None:
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	308 --regions-file '$regions_path'
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	309 #else:
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	310 --regions-file '$section.regions.regions_file'
cfc3a6940b18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e iuc parents: 4 diff changeset	311 #end if
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	312 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	313 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	314 <xml name="macro_targets_file">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	315 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	316 <yield/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	317 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	318 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	319 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	320 <token name="@PREPARE_TARGETS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	321 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	322 #set $targets_path = None
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	323 #if 'targets' in $section
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	324 #if $section.targets.targets_src == 'targets_file':
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	325 #set $targets_path = 'targets_file.tab.gz'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	326 bgzip -c "$section.targets.targets_file" > $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	327 tabix -s 1 -b 2 -e 2 $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	328 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	329 #elif $tgts_sec.targets_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	330 #set $targets_path = 'targets_file.tab.gz'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	331 bgzip -c "$section.targets_file" > $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	332 tabix -s 1 -b 2 -e 2 $targets_path &&
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	333 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	334 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	335 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	336 <token name="@TARGETS_FILE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	337 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	338 #if $targets_path is not None:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	339 --targets-file "${section.invert_targets_file}${targets_path}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	340 #elif $section.targets_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	341 --targets-file "${section.invert_targets_file}${section.targets_file}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	342 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	343 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	344 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	345
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	346 <xml name="macro_targets">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	347 <conditional name="targets">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	348 <param name="targets_src" type="select" label="Targets">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	349 <option value="__none__">None</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	350 <option value="targets">targets</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	351 <option value="targets_file">targets-file</option>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	352 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	353 <when value="__none__"/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	354 <when value="targets">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	355 <param name="targets" type="text" value="" optional="true" label="Restrict to comma-separated list of targets"
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	356 help="Each target is specifed as: chr or chr:pos or chr:from-to">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	357 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	358 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	359 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	360 </when>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	361 <when value="targets_file">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	362 <expand macro="macro_targets_file">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	363 </expand>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	364 </when>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	365 </conditional>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	366 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	367 <token name="@TARGETS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	368 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	369 #if $targets_path:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	370 --targets-file "${section.targets.invert_targets_file}${targets_path}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	371 #else:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	372 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	373 --targets '${section.targets.invert_targets_file}${section.targets.targets}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	374 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	375 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	376 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	377 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	378 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	379 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	380
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	381 <xml name="macro_samples">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	382 <param argument="--samples" type="text" value="" optional="true" label="Samples"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	383 help="Comma separated list of samples to annotate (or exclude)">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	384 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	385 </param>
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	386 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	387 help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" />
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	388 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	389 help="File of samples to include" />
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	390 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	391 help="inverts the query/filtering applied by Samples file" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	392 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	393 <token name="@SAMPLES@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	394 #set $samples_defined = False
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	395 #if str($section.samples) != '':
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	396 #set $samples_defined = True
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	397 --samples '${section.invert_samples}${section.samples}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	398 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	399 #if $section.samples_file:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	400 #set $samples_defined = True
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	401 --samples-file "${section.invert_samples_file}${section.samples_file}"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	402 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	403 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	404
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	405 <xml name="macro_sample">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	406 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" />
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	407 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	408 <token name="@SAMPLE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	409 #if $section.sample:
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	410 --sample '${section.sample}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	411 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	412 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	413
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	414
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	415 <xml name="macro_include">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	416 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	417 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	418 <sanitizer sanitize="False"/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	419 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	420 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	421 <token name="@INCLUDE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	422 #if $section.include:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	423 --include '${section.include}'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	424 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	425 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	426
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	427 <xml name="macro_exclude">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	428 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	429 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	430 <sanitizer sanitize="False"/>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	431 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	432 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	433 <token name="@EXCLUDE@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	434 #if $section.exclude:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	435 --exclude '${section.exclude}'
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	436 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	437 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	438
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	439 <xml name="macro_columns">
7 709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	440 <param name="columns" type="text" value="" optional="true" label="Columns"
709dd8291b83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69 iuc parents: 6 diff changeset	441 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	442 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	443 </param>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	444 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	445 <token name="@COLUMNS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	446 #if $section.columns != '':
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	447 --columns '${section.columns}'
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	448 #end if
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	449 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	450
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	451 <xml name="macro_haploid2diploid">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	452 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	453 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	454
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	455 <xml name="macro_vcf_ids">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	456 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	457 </xml>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	458 <token name="@VCF_IDS@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	459 ${section.vcf_ids}
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	460 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	461
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	462 <token name="@OUTPUT_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	463 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	464 Output Type
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	465 -----------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	466
3 5189d9d9a1dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	467 Output compressed BCF (b), or uncompressed VCF (v).
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	468 Use the BCF option when piping between bcftools subcommands to speed up
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	469 performance by removing unecessary compression/decompression
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	470 and VCF<->BCF conversion.
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	471
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	472 This Galaxy tool recommends using the compressed BCF format
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	473 as piping is not implemented, and uncompressed data would
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	474 use unnecessary amounts of space.
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	475 ]]></token>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	476 <token name="@REGIONS_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	477 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	478 Region Selections
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	479 -----------------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	480
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	481 Regions can be specified in a VCF,
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	482 BED, or tab-delimited file (the default). The columns of the
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	483 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	484 where positions are 1-based and inclusive. Uncompressed
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	485 files are stored in memory, while bgzip-compressed and
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	486 tabix-indexed region files are streamed. Note that sequence
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	487 names must match exactly, "chr20" is not the same as "20".
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	488 Also note that chromosome ordering in FILE will be
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	489 respected, the VCF will be processed in the order in which
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	490 chromosomes first appear in FILE. However, within
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	491 chromosomes, the VCF will always be processed in ascending
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	492 genomic coordinate order no matter what order they appear in
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	493 FILE. Note that overlapping regions in FILE can result in
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	494 duplicated out of order positions in the output. This option
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	495 requires indexed VCF/BCF files.
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	496 ]]></token>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	497 <token name="@TARGETS_HELP@"><![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	498 Targets
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	499 -------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	500
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	501 Similar to regions, but the next position is accessed by streaming the whole
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	502 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	503 applied simultaneously: regions uses the index to jump to a region and targets discards
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	504 positions which are not in the targets. Unlike regions, targets can be prefixed with
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	505 "^" to request logical complement. For example, "^X,Y,MT" indicates that
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	506 sequences X, Y and MT should be skipped. Yet another difference between the two
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	507 is that regions checks both start and end positions of indels, whereas targets checks
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	508 start positions only.
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	509
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	510 For the bcftools call command, with the option -C alleles, third column of the
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	511 targets file must be comma-separated list of alleles, starting with the
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	512 reference allele. Note that the file must be compressed and index. Such a file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	513 can be easily created from a VCF using::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	514
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	515 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf \| bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	516 ]]>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	517 <!-- TODO: galaxy-ify -->
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	518 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	519
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	520
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	521 <token name="@COLLAPSE_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	522 Collapse
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	523 --------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	524
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	525 Controls how to treat records with duplicate positions and defines compatible
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	526 records across multiple input files. Here by "compatible" we mean records which
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	527 should be considered as identical by the tools. For example, when performing
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	528 line intersections, the desire may be to consider as identical all sites with
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	529 matching positions (bcftools isec -c all), or only sites with matching variant
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	530 type (bcftools isec -c snps -c indels), or only sites with all alleles
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	531 identical (bcftools isec -c none).
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	532
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	533
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	534 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	535 \| Flag value \| Result \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	536 +============+================================================================+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	537 \| none \| only records with identical REF and ALT alleles are compatible \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	538 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	539 \| some \| only records where some subset of ALT alleles match are \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	540 \| \| compatible \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	541 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	542 \| all \| all records are compatible, regardless of whether the ALT \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	543 \| \| alleles match or not. In the case of records with the same \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	544 \| \| position, only the first wil lbe considered and appear on \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	545 \| \| output. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	546 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	547 \| snps \| any SNP records are compatible, regardless of whether the ALT \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	548 \| \| alleles match or not. For duplicate positions, only the first \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	549 \| \| SNP record will be considered and appear on output. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	550 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	551 \| indels \| all indel records are compatible, regardless of whether the \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	552 \| \| REF and ALT alleles match or not. For duplicate positions, \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	553 \| \| only the first indel record will be considered and appear on \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	554 \| \| output. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	555 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	556 \| both \| abbreviation of "-c indels -c snps" \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	557 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	558 \| id \| only records with identical ID column are compatible. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	559 \| \| Supportedby bcftools merge only. \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	560 +------------+----------------------------------------------------------------+
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	561 </token>
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	562
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	563 <token name="@EXPRESSIONS_HELP@">
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	564 <![CDATA[
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	565 Expressions
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	566 -----------
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	567
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	568 Valid expressions may contain:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	569
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	570 - numerical constants, string constants
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	571
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	572 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	573
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	574 1, 1.0, 1e-4
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	575 "String"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	576
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	577 - arithmetic operators
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	578
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	579 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	580
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	581 +,*,-,/
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	582
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	583 - comparison operators
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	584
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	585 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	586
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	587 == (same as =), >, >=, <=, <, !=
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	588
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	589 - regex operators "~" and its negation "!~"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	590
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	591 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	592
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	593 INFO/HAYSTACK ~ "needle"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	594
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	595 - parentheses
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	596
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	597 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	598
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	599 (, )
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	600
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	601 - logical operators
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	602
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	603 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	604
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	605 && (same as &), \|\|, \|
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	606
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	607 - INFO tags, FORMAT tags, column names
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	608
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	609 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	610
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	611 INFO/DP or DP
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	612 FORMAT/DV, FMT/DV, or DV
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	613 FILTER, QUAL, ID, REF, ALT[0]
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	614
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	615 - 1 (or 0) to test the presence (or absence) of a flag
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	616
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	617 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	618
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	619 FlagA=1 && FlagB=0
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	620
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	621 - "." to test missing values
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	622
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	623 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	624
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	625 DP=".", DP!=".", ALT="."
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	626
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	627 - missing genotypes can be matched regardless of phase and ploidy (".\|.", "./.", ".") using this expression
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	628
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	629 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	630
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	631 GT="."
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	632
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	633 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	634
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	635 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	636
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	637 TYPE="indel" \| TYPE="snp"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	638
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	639 - array subscripts, "*" for any field
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	640
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	641 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	642
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	643 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	644 DP4[*] == 0
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	645 CSQ[] ~ "missense_variant.deleterious"
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	646
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	647 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	648
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	649 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	650
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	651 MAX, MIN, AVG, SUM, STRLEN, ABS
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	652
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	653 - variables calculated on the fly if not present: number of alternate alleles; number of samples; count of alternate alleles; minor allele count (similar to AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	654
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	655 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	656
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	657 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	658
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	659 Notes:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	660
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	661 - String comparisons and regular expressions are case-insensitive
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	662 - If the subscript "*" is used in regular expression search, the whole field
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	663 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	664 true for the string vector INFO/STR=AB,CD.
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	665 - Variables and function names are case-insensitive, but not tag names. For
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	666 example, "qual" can be used instead of "QUAL", "strlen()" instead of
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	667 "STRLEN()" , but not "dp" instead of "DP".
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	668
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	669 Examples:
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	670
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	671 ::
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	672
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	673 MIN(DV)>5
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	674 MIN(DV/DP)>0.3
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	675 MIN(DP)>10 & MIN(DV)>3
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	676 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	677 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	678 QUAL>10 \| FMT/GQ>10 .. selects only GQ>10 samples
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	679 QUAL>10 \|\| FMT/GQ>10 .. selects all samples at QUAL>10 sites
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	680 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	681 MIN(DP)>35 && AVG(GQ)>50
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	682 ID=@file .. selects lines with ID present in the file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	683 ID!=@~/file .. skip lines with ID present in the ~/file
a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	684 MAF[0]<0.05 .. select rare variants at 5% cutoff
4 71747e4a4aa1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7 iuc parents: 3 diff changeset	685 ]]></token>
0 a994b57c9a7d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	686 </macros>

Mercurial > repos > iuc > bcftools_isec

annotate macros.xml @ 7:709dd8291b83 draft