bcftools_plugin_tag2tag: macros.xml annotate

annotate macros.xml @ 3:24c81c5fcbb5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e

author	iuc
date	Tue, 31 Jan 2017 12:45:37 -0500
parents	8240064eaa73
children	09533c5972fb

rev	line source
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	1
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	2 <macros>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	3 <token name="@VERSION@">1.3</token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	4 <xml name="stdio">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	5 <stdio>
702c96a52e74 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:" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	7 <exit_code range=":-1" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	8 <regex match="Error:" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	9 <regex match="Exception:" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	10 </stdio>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	11 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	12 <xml name="requirements">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	13 <requirements>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	14 <requirement type="package" version="1.3">bcftools</requirement>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	15 <!-- conda dependency -->
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	16 <requirement type="package" version="1.3">htslib</requirement>
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	17 <!-- htslib provides tabix and bgzip
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	18 <requirement type="package" version="0.2.6">tabix</requirement>
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	19 -->
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	20 <requirement type="package" version="1.2">samtools</requirement>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	21 </requirements>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	22 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	23 <xml name="version_command">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	24 <version_command>bcftools 2>&1 \| grep 'Version:'</version_command>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	25 </xml>
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	26
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	27 <xml name="citations">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	28 <citations>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	29 <citation type="doi">10.1093/bioinformatics/btp352</citation>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	30 <yield />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	31 </citations>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	32 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	33 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	34 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	35 <token name="@THREADS@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	36 --threads \${GALAXY_SLOTS:-4}
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	37 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	38 <token name="@PREPARE_ENV@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	39 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	40 export BCFTOOLS_PLUGINS=`which bcftools \| sed 's,bin/bcftools,libexec/bcftools,'`;
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	41 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	42 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	43 <xml name="macro_input">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	44 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	45 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	46 <token name="@PREPARE_INPUT_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	47 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	48 ## May need to symlink input if there is an associated
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	49 #set $input_vcf = 'input.vcf.gz'
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	50 #if $input_file.is_of_type('vcf')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	51 bgzip -c "$input_file" > $input_vcf &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	52 bcftools index $input_vcf &&
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	53 #elif $input_file.is_of_type('vcf_bgzip')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	54 ln -s "$input_file" $input_vcf
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	55 #elif $input_file.is_of_type('bcf')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	56 #set $input_vcf = 'input.bcf'
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	57 ln -s "$input_file" $input_vcf &&
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	58 #if $input_file.metadata.bcf_index:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	59 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	60 #else
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	61 bcftools index $input_vcf &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	62 #end if
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	63 #elif $input_file.is_of_type('bcf_bgzip')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	64 ln -s "$input_file" $input_vcf
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	65 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	66 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	67 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	68 <token name="@INPUT_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	69 $input_vcf
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	70 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	71
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	72 <xml name="macro_inputs">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	73 <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	74 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	75 <token name="@PREPARE_INPUT_FILES@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	76 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	77 ## May need to symlink input if there is an associated
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	78 #set $input_vcfs = []
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	79 #set $vcfs_list_file = 'vcfs_list'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	80 #for (i,input_file) in enumerate($input_files):
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	81 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	82 #if $input_file.is_of_type('vcf')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	83 bgzip -c "$input_file" > $input_vcf &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	84 bcftools index $input_vcf &&
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	85 #elif $input_file.is_of_type('vcf_bgz')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	86 ln -s "$input_file" $input_vcf
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	87 #elif $input_file.is_of_type('bcf')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	88 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	89 ## bgzip -c "$input_file" > $input_vcf &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	90 ln -s "$input_file" $input_vcf &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	91 #if $input_file.metadata.bcf_index:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	92 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	93 #else
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	94 bcftools index $input_vcf &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	95 #end if
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	96 #elif $input_file.is_of_type('bcfvcf_bgz')
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	97 ln -s "$input_file" $input_vcf &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	98 #end if
1 24795ba8730c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06 iuc parents: 0 diff changeset	99 echo '$input_vcf' >> $vcfs_list_file &&
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	100 $input_vcfs.append($input_vcf)
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	101 #end for
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	102 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	103 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	104 <token name="@INPUT_FILES@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	105 #echo ' '.join($input_vcfs)#
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	106 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	107 <token name="@INPUT_LIST_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	108 $vcfs_list_file
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	109 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	110
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	111 <xml name="macro_fasta_ref">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	112 <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	113 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	114 <token name="@PREPARE_FASTA_REF@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	115 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	116 #set $input_fa_ref = None
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	117 #if 'fasta_ref' in $section and $section.fasta_ref:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	118 #set $input_fa_ref = 'ref.fa'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	119 ln -s $section.fasta_ref $input_fa_ref &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	120 samtools faidx $input_fa_ref &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	121 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	122 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	123 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	124 <token name="@FASTA_REF@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	125 #if $input_fa_ref is not None:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	126 --fasta-ref "$input_fa_ref"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	127 #elif 'fasta_ref' in $section and $section.fasta_ref:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	128 --fasta-ref "${section.fasta_ref}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	129 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	130 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	131
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	132 <xml name="macro_ref_fasta">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	133 <conditional name="reference_source">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	134 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	135 <option value="cached">Locally cached</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	136 <option value="history">History</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	137 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	138 <when value="cached">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	139 <param name="ref_file" type="select" label="Select reference genome">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	140 <options from_data_table="fasta_indexes">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	141 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	142 </options>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	143 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	144 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	145 </when>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	146 <when value="history"> <!-- FIX ME!!!! -->
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	147 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	148 </when>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	149 </conditional>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	150 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	151
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	152
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	153 <xml name="macro_AF_file">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	154 <param name="AF_file" type="data" format="data" label="Af File" optional="True" help="read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	155 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	156 <!-- This may need to bgzip and tabix the file -->
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	157 <token name="@PREPARE_AF_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	158 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	159 #if 'AF_file' in $section and $section.AF_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	160 #pass
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	161 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	162 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	163 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	164 <token name="@AF_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	165 #if 'AF_file' in $section and $section.AF_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	166 --AF-file "${section.AF_file}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	167 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	168 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	169
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	170 <xml name="macro_estimate_AF">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	171 <param name="estimate_AF" type="data" format="data" label="Estimate Af" optional="True" help="calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	172 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	173 <token name="@ESTIMATE_AF@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	174 #if 'estimate_AF' in $section and $section.estimate_AF:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	175 --estimate-AF "${section.estimate_AF}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	176 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	177 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	178
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	179 <xml name="macro_exons_file">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	180 <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	181 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	182 <token name="@PREPARE_EXONS_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	183 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	184 #set $exons_path = None
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	185 #if 'exons_file' in $section and $section.exons_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	186 #set $exons_path = 'exons_file.tab.gz'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	187 bgzip -c "$section.exons_file" > $exons_path &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	188 tabix -s 1 -b 2 -e 3 $exons_path &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	189 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	190 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	191 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	192 <token name="@EXONS_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	193 #if 'exons_file' in $section and $section.exons_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	194 --exons $exons_path
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	195 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	196 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	197
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	198 <xml name="macro_ploidy_file">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	199 <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	200 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	201 <token name="@PLOIDY_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	202 #if 'ploidy_file' in $section and $section.ploidy_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	203 --ploidy "${section.ploidy_file}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	204 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	205 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	206
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	207 <xml name="macro_collapse_opt_none">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	208 <option value="none">none - require the exact same set of alleles in all files</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	209 </xml>
702c96a52e74 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_id">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	211 <option value="id">id - only records with identical ID column are compatible. </option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	212 </xml>
702c96a52e74 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">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	214 <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	215 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	216 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	217 <option value="both">both - indels and snps </option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	218 <option value="some">some - at least some of the ALTs must match</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	219 <option value="any">any - any combination of alleles</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	220 <yield/>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	221 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	222 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	223 <token name="@COLLAPSE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	224 #if $section.collapse:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	225 --collapse "${section.collapse}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	226 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	227 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	228
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	229 <xml name="macro_apply_filters">
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	230 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	231 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	232 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	233 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	234 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	235 <token name="@APPLY_FILTERS@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	236 #if $section.apply_filters:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	237 --apply-filters "${section.apply_filters}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	238 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	239 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	240
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	241 <xml name="macro_select_output_type">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	242 <param name="output_type" type="select">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	243 <option value="b">compressed BCF</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	244 <!-- no galaxy datatypes for these
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	245 <option value="u">uncompressed BCF</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	246 <option value="z">compressed VCF</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	247 -->
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	248 <option value="v">uncompressed VCF</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	249 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	250 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	251 <token name="@OUTPUT_TYPE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	252 #if str($output_type) != "__none__":
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	253 --output-type "${output_type}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	254 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	255 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	256
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	257 <xml name="macro_vcf_output">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	258 <data name="output_file" format="vcf">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	259 <change_format>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	260 <when input="output_type" value="b" format="bcf" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	261 <when input="output_type" value="u" format="bcf" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	262 <when input="output_type" value="z" format="vcf_bgzip" />
702c96a52e74 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="v" format="vcf" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	264 </change_format>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	265 </data>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	266 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	267
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	268 <xml name="macro_regions">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	269 <conditional name="regions">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	270 <param name="regions_src" type="select" label="Regions">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	271 <option value="__none__">None</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	272 <option value="regions">regions</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	273 <option value="regions_file">regions-file</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	274 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	275 <when value="__none__"/>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	276 <when value="regions">
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	277 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	278 help="Each region is specifed as: chr or chr:pos or chr:from-to">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	279 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	280 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	281 </when>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	282 <when value="regions_file">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	283 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	284 </when>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	285 </conditional>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	286 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	287 <token name="@REGIONS@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	288 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	289 --regions "$section.regions.regions"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	290 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	291 --regions-file "$section.regions.regions_file"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	292 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	293 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	294
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	295 <xml name="macro_targets_file">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	296 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	297 <yield/>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	298 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	299 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	300 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	301 <token name="@PREPARE_TARGETS_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	302 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	303 #set $targets_path = None
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	304 #if 'targets' in $section
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	305 #if $section.targets.targets_src == 'targets_file':
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	306 #set $targets_path = 'targets_file.tab.gz'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	307 bgzip -c "$section.targets.targets_file" > $targets_path &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	308 tabix -s 1 -b 2 -e 2 $targets_path &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	309 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	310 #elif $tgts_sec.targets_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	311 #set $targets_path = 'targets_file.tab.gz'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	312 bgzip -c "$section.targets_file" > $targets_path &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	313 tabix -s 1 -b 2 -e 2 $targets_path &&
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	314 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	315 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	316 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	317 <token name="@TARGETS_FILE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	318 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	319 #if $targets_path is not None:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	320 --targets-file "${section.invert_targets_file}${targets_path}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	321 #elif $section.targets_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	322 --targets-file "${section.invert_targets_file}${section.targets_file}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	323 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	324 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	325 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	326
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	327 <xml name="macro_targets">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	328 <conditional name="targets">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	329 <param name="targets_src" type="select" label="Targets">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	330 <option value="__none__">None</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	331 <option value="targets">targets</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	332 <option value="targets_file">targets-file</option>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	333 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	334 <when value="__none__"/>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	335 <when value="targets">
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	336 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	337 help="Each target is specifed as: chr or chr:pos or chr:from-to">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	338 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	339 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	340 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	341 </when>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	342 <when value="targets_file">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	343 <expand macro="macro_targets_file">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	344 </expand>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	345 </when>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	346 </conditional>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	347 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	348 <token name="@TARGETS@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	349 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	350 #if $targets_path:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	351 --targets-file "${section.targets.invert_targets_file}${targets_path}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	352 #else:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	353 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	354 --targets "${section.targets.invert_targets_file}${section.targets.targets}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	355 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	356 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	357 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	358 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	359 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	360 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	361
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	362 <xml name="macro_samples">
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	363 <param name="samples" type="text" value="" label="Samples" optional="true"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	364 help="(-s) comma separated list of samples to annotate (or exclude with "^" prefix)">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	365 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	366 </param>
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	367 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	368 help="inverts the query/filtering applied by Samples" />
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	369 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	370 help="(-S) file of samples to include" />
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	371 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	372 help="inverts the query/filtering applied by Samples File" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	373 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	374 <token name="@SAMPLES@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	375 #set $samples_defined = False
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	376 #if str($section.samples) != '':
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	377 #set $samples_defined = True
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	378 --samples "${section.invert_samples}${section.samples}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	379 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	380 #if $section.samples_file:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	381 #set $samples_defined = True
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	382 --samples-file "${section.invert_samples_file}${section.samples_file}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	383 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	384 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	385
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	386 <xml name="macro_sample">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	387 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	388 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	389 <token name="@SAMPLE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	390 #if $section.sample:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	391 --sample "${section.sample}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	392 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	393 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	394
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	395
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	396 <xml name="macro_include">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	397 <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	398 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	399 <sanitizer sanitize="False"/>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	400 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	401 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	402 <token name="@INCLUDE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	403 #if $section.include:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	404 --include '${section.include}'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	405 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	406 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	407
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	408 <xml name="macro_exclude">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	409 <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	410 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	411 <sanitizer sanitize="False"/>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	412 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	413 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	414 <token name="@EXCLUDE@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	415 #if $section.exclude:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	416 --exclude '${section.exclude}'
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	417 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	418 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	419
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	420 <xml name="macro_columns">
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	421 <param name="columns" type="text" value="" label="Columns" optional="true"
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	422 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	423 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	424 </param>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	425 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	426 <token name="@COLUMNS@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	427 #if $section.columns != '':
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	428 --columns "${section.columns}"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	429 #end if
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	430 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	431
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	432 <xml name="macro_haploid2diploid">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	433 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	434 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	435
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	436 <xml name="macro_vcf_ids">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	437 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	438 </xml>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	439 <token name="@VCF_IDS@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	440 ${section.vcf_ids}
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	441 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	442
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	443 <token name="@OUTPUT_HELP@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	444 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	445 Output Type
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	446 -----------
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	447
3 24c81c5fcbb5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e iuc parents: 2 diff changeset	448 Output compressed BCF (b), or uncompressed VCF (v).
0 702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	449 Use the BCF option when piping between bcftools subcommands to speed up
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	450 performance by removing unecessary compression/decompression
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	451 and VCF<->BCF conversion.
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	452
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	453 This Galaxy tool recommends using the compressed BCF format
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	454 as piping is not implemented, and uncompressed data would
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	455 use unnecessary amounts of space.
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	456
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	457 ]]></token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	458 <token name="@REGIONS_HELP@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	459 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	460 Region Selections
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	461 -----------------
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	462
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	463 Regions can be specified in a VCF,
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	464 BED, or tab-delimited file (the default). The columns of the
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	465 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	466 where positions are 1-based and inclusive. Uncompressed
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	467 files are stored in memory, while bgzip-compressed and
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	468 tabix-indexed region files are streamed. Note that sequence
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	469 names must match exactly, "chr20" is not the same as "20".
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	470 Also note that chromosome ordering in FILE will be
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	471 respected, the VCF will be processed in the order in which
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	472 chromosomes first appear in FILE. However, within
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	473 chromosomes, the VCF will always be processed in ascending
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	474 genomic coordinate order no matter what order they appear in
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	475 FILE. Note that overlapping regions in FILE can result in
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	476 duplicated out of order positions in the output. This option
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	477 requires indexed VCF/BCF files.
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	478
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	479 ]]></token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	480 <token name="@TARGETS_HELP@"><![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	481 Targets
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	482 -------
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	483
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	484 Similar to regions, but the next position is accessed by streaming the whole
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	485 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	486 applied simultaneously: regions uses the index to jump to a region and targets discards
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	487 positions which are not in the targets. Unlike regions, targets can be prefixed with
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	488 "^" to request logical complement. For example, "^X,Y,MT" indicates that
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	489 sequences X, Y and MT should be skipped. Yet another difference between the two
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	490 is that regions checks both start and end positions of indels, whereas targets checks
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	491 start positions only.
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	492
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	493 For the bcftools call command, with the option -C alleles, third column of the
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	494 targets file must be comma-separated list of alleles, starting with the
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	495 reference allele. Note that the file must be compressed and index. Such a file
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	496 can be easily created from a VCF using::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	497
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	498 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf \| bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	499 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	500 <!-- TODO: galaxy-ify -->
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	501 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	502
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	503
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	504 <token name="@COLLAPSE_HELP@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	505 Collapse
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	506 --------
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	507
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	508 Controls how to treat records with duplicate positions and defines compatible
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	509 records across multiple input files. Here by "compatible" we mean records which
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	510 should be considered as identical by the tools. For example, when performing
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	511 line intersections, the desire may be to consider as identical all sites with
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	512 matching positions (bcftools isec -c all), or only sites with matching variant
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	513 type (bcftools isec -c snps -c indels), or only sites with all alleles
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	514 identical (bcftools isec -c none).
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	515
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	516
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	517 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	518 \| Flag value \| Result \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	519 +============+================================================================+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	520 \| none \| only records with identical REF and ALT alleles are compatible \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	521 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	522 \| some \| only records where some subset of ALT alleles match are \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	523 \| \| compatible \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	524 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	525 \| all \| all records are compatible, regardless of whether the ALT \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	526 \| \| alleles match or not. In the case of records with the same \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	527 \| \| position, only the first wil lbe considered and appear on \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	528 \| \| output. \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	529 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	530 \| snps \| any SNP records are compatible, regardless of whether the ALT \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	531 \| \| alleles match or not. For duplicate positions, only the first \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	532 \| \| SNP record will be considered and appear on output. \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	533 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	534 \| indels \| all indel records are compatible, regardless of whether the \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	535 \| \| REF and ALT alleles match or not. For duplicate positions, \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	536 \| \| only the first indel record will be considered and appear on \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	537 \| \| output. \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	538 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	539 \| both \| abbreviation of "-c indels -c snps" \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	540 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	541 \| id \| only records with identical ID column are compatible. \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	542 \| \| Supportedby bcftools merge only. \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	543 +------------+----------------------------------------------------------------+
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	544
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	545 </token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	546
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	547 <token name="@EXPRESSIONS_HELP@">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	548 <![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	549 Expressions
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	550 -----------
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	551
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	552 Valid expressions may contain:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	553
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	554 - numerical constants, string constants
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	555
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	556 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	557
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	558 1, 1.0, 1e-4
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	559 "String"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	560
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	561 - arithmetic operators
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	562
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	563 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	564
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	565 +,*,-,/
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	566
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	567 - comparison operators
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	568
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	569 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	570
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	571 == (same as =), >, >=, <=, <, !=
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	572
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	573 - regex operators "~" and its negation "!~"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	574
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	575 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	576
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	577 INFO/HAYSTACK ~ "needle"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	578
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	579 - parentheses
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	580
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	581 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	582
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	583 (, )
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	584
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	585 - logical operators
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	586
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	587 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	588
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	589 && (same as &), \|\|, \|
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	590
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	591 - INFO tags, FORMAT tags, column names
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	592
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	593 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	594
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	595 INFO/DP or DP
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	596 FORMAT/DV, FMT/DV, or DV
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	597 FILTER, QUAL, ID, REF, ALT[0]
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	598
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	599 - 1 (or 0) to test the presence (or absence) of a flag
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	600
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	601 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	602
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	603 FlagA=1 && FlagB=0
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	604
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	605 - "." to test missing values
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	606
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	607 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	608
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	609 DP=".", DP!=".", ALT="."
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	610
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	611 - missing genotypes can be matched regardless of phase and ploidy (".\|.", "./.", ".") using this expression
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	612
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	613 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	614
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	615 GT="."
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	616
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	617 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	618
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	619 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	620
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	621 TYPE="indel" \| TYPE="snp"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	622
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	623 - array subscripts, "*" for any field
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	624
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	625 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	626
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	627 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	628 DP4[*] == 0
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	629 CSQ[] ~ "missense_variant.deleterious"
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	630
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	631 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	632
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	633 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	634
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	635 MAX, MIN, AVG, SUM, STRLEN, ABS
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	636
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	637 - 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
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	638
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	639 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	640
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	641 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	642
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	643 Notes:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	644
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	645 - String comparisons and regular expressions are case-insensitive
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	646 - If the subscript "*" is used in regular expression search, the whole field
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	647 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	648 true for the string vector INFO/STR=AB,CD.
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	649 - Variables and function names are case-insensitive, but not tag names. For
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	650 example, "qual" can be used instead of "QUAL", "strlen()" instead of
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	651 "STRLEN()" , but not "dp" instead of "DP".
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	652
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	653 Examples:
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	654
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	655 ::
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	656
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	657 MIN(DV)>5
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	658 MIN(DV/DP)>0.3
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	659 MIN(DP)>10 & MIN(DV)>3
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	660 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	661 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	662 QUAL>10 \| FMT/GQ>10 .. selects only GQ>10 samples
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	663 QUAL>10 \|\| FMT/GQ>10 .. selects all samples at QUAL>10 sites
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	664 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	665 MIN(DP)>35 && AVG(GQ)>50
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	666 ID=@file .. selects lines with ID present in the file
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	667 ID!=@~/file .. skip lines with ID present in the ~/file
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	668 MAF[0]<0.05 .. select rare variants at 5% cutoff
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	669
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	670 ]]></token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	671
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	672
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	673
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	674
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: diff changeset	675 </macros>

Mercurial > repos > iuc > bcftools_plugin_tag2tag

annotate macros.xml @ 3:24c81c5fcbb5 draft