bcftools_call: macros.xml annotate

annotate macros.xml @ 3:5337db17a5f7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 44bebb8a97d64015cbba59f0663e2541035112b6

author	iuc
date	Mon, 03 Oct 2016 12:19:38 -0400
parents	99dff9c8b2f3
children	6d2a5f0859cf

rev	line source
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	1
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	2 <macros>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	3 <token name="@VERSION@">1.3</token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	4 <xml name="stdio">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	5 <stdio>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	6 <exit_code range="1:" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	7 <exit_code range=":-1" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	8 <regex match="Error:" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	9 <regex match="Exception:" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	10 </stdio>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	11 </xml>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	12 <xml name="requirements">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	13 <requirements>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	14 <requirement type="package" version="1.3">bcftools</requirement>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	15 <!-- conda dependency -->
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	16 <requirement type="package" version="1.3">htslib</requirement>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	17 <requirement type="package" version="0.2.6">tabix</requirement>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	18 <requirement type="package" version="1.2">samtools</requirement>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	19 </requirements>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	20 </xml>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	21 <xml name="version_command">
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	22 <version_command>bcftools 2>&1 \| grep 'Version:'</version_command>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	23 </xml>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	24
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	25 <xml name="citations">
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	26 <citations>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	27 <citation type="doi">10.1093/bioinformatics/btp352</citation>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	28 <yield />
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	29 </citations>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	30 </xml>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	31 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	32 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	33 <token name="@THREADS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	34 --threads \${GALAXY_SLOTS:-4}
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	35 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	36 <token name="@PREPARE_ENV@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	37 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	38 export BCFTOOLS_PLUGINS=`which bcftools \| sed 's,bin/bcftools,libexec/bcftools,'`;
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	39 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	40 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	41 <xml name="macro_input">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	43 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	44 <token name="@PREPARE_INPUT_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	45 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	46 ## May need to symlink input if there is an associated
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	47 #set $input_vcf = 'input.vcf.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	48 #if $input_file.datatype.file_ext == 'vcf'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	49 bgzip -c "$input_file" > $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	50 bcftools index $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	51 #elif $input_file.datatype.file_ext == 'vcf_bgzip'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	52 ln -s "$input_file" $input_vcf
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	53 #elif $input_file.datatype.file_ext == 'bcf'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	54 #set $input_vcf = 'input.bcf'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	55 ln -s "$input_file" $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	56 #if $input_file.metadata.bcf_index:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	57 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	58 #else
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	59 bcftools index $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	60 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	61 #elif $input_file.datatype.file_ext == 'bcf_bgzip'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	62 ln -s "$input_file" $input_vcf
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	63 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	64 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	65 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	66 <token name="@INPUT_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	67 $input_vcf
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	68 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	69
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	70 <xml name="macro_inputs">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	71 <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	72 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	73 <token name="@PREPARE_INPUT_FILES@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	74 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	75 ## May need to symlink input if there is an associated
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	76 #set $input_vcfs = []
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	77 #set $vcfs_list_file = 'vcfs_list'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	78 #for (i,input_file) in enumerate($input_files):
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	79 #set $input_vcf = 'input' + str($i) + '.vcf.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	80 #if $input_file.datatype.file_ext == 'vcf'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	81 bgzip -c "$input_file" > $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	82 bcftools index $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	83 #elif $input_file.datatype.file_ext == 'vcf_bgz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	84 ln -s "$input_file" $input_vcf
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	85 #elif $input_file.datatype.file_ext == 'bcf'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	86 #set $input_vcf = 'input' + str($i) + '.bcf.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	87 ## bgzip -c "$input_file" > $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	88 ln -s "$input_file" $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	89 #if $input_file.metadata.bcf_index:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	90 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	91 #else
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	92 bcftools index $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	93 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	94 #elif $input_file.datatype.file_ext == 'bcfvcf_bgz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	95 ln -s "$input_file" $input_vcf &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	96 #end if
2 99dff9c8b2f3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06 iuc parents: 1 diff changeset	97 echo '$input_vcf' >> $vcfs_list_file &&
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	98 $input_vcfs.append($input_vcf)
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	99 #end for
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	100 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	101 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	102 <token name="@INPUT_FILES@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	103 #echo ' '.join($input_vcfs)#
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	104 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	105 <token name="@INPUT_LIST_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	106 $vcfs_list_file
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	107 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	108
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	109 <xml name="macro_fasta_ref">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	110 <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	111 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	112 <token name="@PREPARE_FASTA_REF@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	113 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	114 #set $input_fa_ref = None
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	115 #if 'fasta_ref' in $section and $section.fasta_ref:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	116 #set $input_fa_ref = 'ref.fa'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	117 ln -s $section.fasta_ref $input_fa_ref &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	118 samtools faidx $input_fa_ref &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	119 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	120 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	121 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	122 <token name="@FASTA_REF@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	123 #if $input_fa_ref is not None:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	124 --fasta-ref "$input_fa_ref"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	125 #elif 'fasta_ref' in $section and $section.fasta_ref:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	126 --fasta-ref "${section.fasta_ref}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	127 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	128 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	129
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	130 <xml name="macro_ref_fasta">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	131 <conditional name="reference_source">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	132 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	133 <option value="cached">Locally cached</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	134 <option value="history">History</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	135 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	136 <when value="cached">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	137 <param name="ref_file" type="select" label="Select reference genome">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	138 <options from_data_table="fasta_indexes">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	139 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	140 </options>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	141 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	142 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	143 </when>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	144 <when value="history"> <!-- FIX ME!!!! -->
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	145 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	146 </when>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	147 </conditional>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	148 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	149
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	150
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	151 <xml name="macro_AF_file">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	152 <param name="AF_file" type="data" format="data" label="Af File" optional="True" help="read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	153 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	154 <!-- This may need to bgzip and tabix the file -->
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	155 <token name="@PREPARE_AF_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	156 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	157 #if 'AF_file' in $section and $section.AF_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	158 #pass
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	159 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	160 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	161 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	162 <token name="@AF_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	163 #if 'AF_file' in $section and $section.AF_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	164 --AF-file "${section.AF_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	165 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	166 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	167
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	168 <xml name="macro_estimate_AF">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	169 <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>" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	170 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	171 <token name="@ESTIMATE_AF@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	172 #if 'estimate_AF' in $section and $section.estimate_AF:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	173 --estimate-AF "${section.estimate_AF}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	174 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	175 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	176
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	177 <xml name="macro_exons_file">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	178 <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)" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	179 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	180 <token name="@PREPARE_EXONS_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	181 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	182 #set $exons_path = None
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	183 #if 'exons_file' in $section and $section.exons_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	184 #set $exons_path = 'exons_file.tab.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	185 bgzip -c "$section.exons_file" > $exons_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	186 tabix -s 1 -b 2 -e 3 $exons_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	187 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	188 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	189 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	190 <token name="@EXONS_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	191 #if 'exons_file' in $section and $section.exons_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	192 --exons $exons_path
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	193 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	194 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	195
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	196 <xml name="macro_ploidy_file">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	197 <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	198 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	199 <token name="@PLOIDY_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	200 #if 'ploidy_file' in $section and $section.ploidy_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	201 --ploidy "${section.ploidy_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	202 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	203 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	204
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	205 <xml name="macro_collapse_opt_none">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	206 <option value="none">none - require the exact same set of alleles in all files</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	207 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	208 <xml name="macro_collapse_opt_id">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	209 <option value="id">id - only records with identical ID column are compatible. </option>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	210 </xml>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	211 <xml name="macro_collapse">
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	212 <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">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	213 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	214 <option value="indels">indels - allow different alleles, as long as they all are indels</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	215 <option value="both">both - indels and snps </option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	216 <option value="some">some - at least some of the ALTs must match</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	217 <option value="any">any - any combination of alleles</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	218 <yield/>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	219 </param>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	220 </xml>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	221 <token name="@COLLAPSE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	222 #if $section.collapse:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	223 --collapse "${section.collapse}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	224 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	225 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	226
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	227 <xml name="macro_apply_filters">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	228 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	229 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	230 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	231 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	232 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	233 <token name="@APPLY_FILTERS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	234 #if $section.apply_filters:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	235 --apply-filters "${section.apply_filters}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	236 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	237 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	238
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	239 <xml name="macro_select_output_type">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	240 <param name="output_type" type="select">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	241 <option value="b">compressed BCF</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	242 <!-- no galaxy datatypes for these
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	243 <option value="u">uncompressed BCF</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	244 <option value="z">compressed VCF</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	245 -->
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	246 <option value="v">uncompressed VCF</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	247 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	248 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	249 <token name="@OUTPUT_TYPE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	250 #if str($output_type) != "__none__":
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	251 --output-type "${output_type}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	252 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	253 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	254
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	255 <xml name="macro_vcf_output">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	256 <data name="output_file" format="vcf">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	257 <change_format>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	258 <when input="output_type" value="b" format="bcf" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	259 <when input="output_type" value="u" format="bcf" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	260 <when input="output_type" value="z" format="vcf_bgzip" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	261 <when input="output_type" value="v" format="vcf" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	262 </change_format>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	263 </data>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	264 </xml>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	265
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	266 <xml name="macro_regions">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	267 <conditional name="regions">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	268 <param name="regions_src" type="select" label="Regions">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	269 <option value="__none__">None</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	270 <option value="regions">regions</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	271 <option value="regions_file">regions-file</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	272 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	273 <when value="__none__"/>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	274 <when value="regions">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	275 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	276 help="Each region is specifed as: chr or chr:pos or chr:from-to">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	277 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	278 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	279 </when>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	280 <when value="regions_file">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	281 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	282 </when>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	283 </conditional>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	284 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	285 <token name="@REGIONS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	286 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	287 --regions "$section.regions.regions"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	288 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	289 --regions-file "$section.regions.regions_file"
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	290 #end if
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	291 </token>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	292
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	293 <xml name="macro_targets_file">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	294 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" >
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	295 <yield/>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	296 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	297 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" />
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	298 </xml>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	299 <token name="@PREPARE_TARGETS_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	300 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	301 #set $targets_path = None
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	302 #if 'targets' in $section
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	303 #if $section.targets.targets_src == 'targets_file':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	304 #set $targets_path = 'targets_file.tab.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	305 bgzip -c "$section.targets.targets_file" > $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	306 tabix -s 1 -b 2 -e 2 $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	307 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	308 #elif $tgts_sec.targets_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	309 #set $targets_path = 'targets_file.tab.gz'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	310 bgzip -c "$section.targets_file" > $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	311 tabix -s 1 -b 2 -e 2 $targets_path &&
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	312 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	313 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	314 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	315 <token name="@TARGETS_FILE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	316 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	317 #if $targets_path is not None:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	318 --targets-file "${section.invert_targets_file}${targets_path}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	319 #elif $section.targets_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	320 --targets-file "${section.invert_targets_file}${section.targets_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	321 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	322 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	323 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	324
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	325 <xml name="macro_targets">
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	326 <conditional name="targets">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	327 <param name="targets_src" type="select" label="Targets">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	328 <option value="__none__">None</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	329 <option value="targets">targets</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	330 <option value="targets_file">targets-file</option>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	331 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	332 <when value="__none__"/>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	333 <when value="targets">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	334 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	335 help="Each target is specifed as: chr or chr:pos or chr:from-to">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	336 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	337 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	338 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	339 </when>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	340 <when value="targets_file">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	341 <expand macro="macro_targets_file">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	342 </expand>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	343 </when>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	344 </conditional>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	345 </xml>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	346 <token name="@TARGETS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	347 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	348 #if $targets_path:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	349 --targets-file "${section.targets.invert_targets_file}${targets_path}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	350 #else:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	351 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	352 --targets "${section.targets.invert_targets_file}${section.targets.targets}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	353 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	354 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	355 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	356 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	357 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	358 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	359
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	360 <xml name="macro_samples">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	361 <param name="samples" type="text" value="" label="Samples" optional="true"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	362 help="(-s) comma separated list of samples to annotate (or exclude with "^" prefix)">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	363 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	364 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	365 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	366 help="inverts the query/filtering applied by Samples" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	367 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	368 help="(-S) file of samples to include" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	369 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	370 help="inverts the query/filtering applied by Samples File" />
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	371 </xml>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	372 <token name="@SAMPLES@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	373 #set $samples_defined = False
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	374 #if str($section.samples) != '':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	375 #set $samples_defined = True
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	376 --samples "${section.invert_samples}${section.samples}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	377 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	378 #if $section.samples_file:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	379 #set $samples_defined = True
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	380 --samples-file "${section.invert_samples_file}${section.samples_file}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	381 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	382 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	383
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	384 <xml name="macro_sample">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	385 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	386 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	387 <token name="@SAMPLE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	388 #if $section.sample:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	389 --sample "${section.sample}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	390 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	391 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	392
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	393
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	394 <xml name="macro_include">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	395 <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	396 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	397 <sanitizer sanitize="False"/>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	398 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	399 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	400 <token name="@INCLUDE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	401 #if $section.include:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	402 --include '${section.include}'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	403 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	404 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	405
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	406 <xml name="macro_exclude">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	407 <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	408 <validator type="regex" message="Single quote not allowed">^[^']*$</validator>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	409 <sanitizer sanitize="False"/>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	410 </param>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	411 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	412 <token name="@EXCLUDE@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	413 #if $section.exclude:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	414 --exclude '${section.exclude}'
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	415 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	416 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	417
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	418 <xml name="macro_columns">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	419 <param name="columns" type="text" value="" label="Columns" optional="true"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	420 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	421 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator>
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	422 </param>
a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	423 </xml>
1 8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	424 <token name="@COLUMNS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	425 #if $section.columns != '':
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	426 --columns "${section.columns}"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	427 #end if
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	428 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	429
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	430 <xml name="macro_haploid2diploid">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	431 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	432 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	433
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	434 <xml name="macro_vcf_ids">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	435 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" />
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	436 </xml>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	437 <token name="@VCF_IDS@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	438 ${section.vcf_ids}
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	439 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	440
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	441 <token name="@OUTPUT_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	442 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	443 Output Type
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	444 -----------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	445
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	446 Output compressed BCF (b), or uncompressed VCF (v).
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	447 Use the BCF option when piping between bcftools subcommands to speed up
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	448 performance by removing unecessary compression/decompression
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	449 and VCF<->BCF conversion.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	450
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	451 This Galaxy tool recommends using the compressed BCF format
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	452 as piping is not implemented, and uncompressed data would
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	453 use unnecessary amounts of space.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	454
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	455 ]]></token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	456 <token name="@REGIONS_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	457 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	458 Region Selections
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	459 -----------------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	460
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	461 Regions can be specified in a VCF,
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	462 BED, or tab-delimited file (the default). The columns of the
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	463 tab-delimited file are: CHROM, POS, and, optionally, POS_TO,
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	464 where positions are 1-based and inclusive. Uncompressed
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	465 files are stored in memory, while bgzip-compressed and
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	466 tabix-indexed region files are streamed. Note that sequence
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	467 names must match exactly, "chr20" is not the same as "20".
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	468 Also note that chromosome ordering in FILE will be
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	469 respected, the VCF will be processed in the order in which
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	470 chromosomes first appear in FILE. However, within
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	471 chromosomes, the VCF will always be processed in ascending
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	472 genomic coordinate order no matter what order they appear in
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	473 FILE. Note that overlapping regions in FILE can result in
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	474 duplicated out of order positions in the output. This option
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	475 requires indexed VCF/BCF files.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	476
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	477 ]]></token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	478 <token name="@TARGETS_HELP@"><![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	479 Targets
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	480 -------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	481
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	482 Similar to regions, but the next position is accessed by streaming the whole
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	483 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	484 applied simultaneously: regions uses the index to jump to a region and targets discards
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	485 positions which are not in the targets. Unlike regions, targets can be prefixed with
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	486 "^" to request logical complement. For example, "^X,Y,MT" indicates that
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	487 sequences X, Y and MT should be skipped. Yet another difference between the two
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	488 is that regions checks both start and end positions of indels, whereas targets checks
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	489 start positions only.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	490
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	491 For the bcftools call command, with the option -C alleles, third column of the
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	492 targets file must be comma-separated list of alleles, starting with the
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	493 reference allele. Note that the file must be compressed and index. Such a file
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	494 can be easily created from a VCF using::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	495
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	496 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf \| bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	497 ]]>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	498 <!-- TODO: galaxy-ify -->
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	499 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	500
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	501
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	502 <token name="@COLLAPSE_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	503 Collapse
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	504 --------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	505
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	506 Controls how to treat records with duplicate positions and defines compatible
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	507 records across multiple input files. Here by "compatible" we mean records which
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	508 should be considered as identical by the tools. For example, when performing
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	509 line intersections, the desire may be to consider as identical all sites with
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	510 matching positions (bcftools isec -c all), or only sites with matching variant
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	511 type (bcftools isec -c snps -c indels), or only sites with all alleles
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	512 identical (bcftools isec -c none).
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	513
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	514
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	515 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	516 \| Flag value \| Result \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	517 +============+================================================================+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	518 \| none \| only records with identical REF and ALT alleles are compatible \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	519 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	520 \| some \| only records where some subset of ALT alleles match are \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	521 \| \| compatible \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	522 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	523 \| all \| all records are compatible, regardless of whether the ALT \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	524 \| \| alleles match or not. In the case of records with the same \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	525 \| \| position, only the first wil lbe considered and appear on \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	526 \| \| output. \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	527 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	528 \| snps \| any SNP records are compatible, regardless of whether the ALT \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	529 \| \| alleles match or not. For duplicate positions, only the first \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	530 \| \| SNP record will be considered and appear on output. \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	531 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	532 \| indels \| all indel records are compatible, regardless of whether the \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	533 \| \| REF and ALT alleles match or not. For duplicate positions, \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	534 \| \| only the first indel record will be considered and appear on \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	535 \| \| output. \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	536 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	537 \| both \| abbreviation of "-c indels -c snps" \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	538 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	539 \| id \| only records with identical ID column are compatible. \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	540 \| \| Supportedby bcftools merge only. \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	541 +------------+----------------------------------------------------------------+
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	542
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	543 </token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	544
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	545 <token name="@EXPRESSIONS_HELP@">
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	546 <![CDATA[
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	547 Expressions
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	548 -----------
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	549
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	550 Valid expressions may contain:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	551
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	552 - numerical constants, string constants
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	553
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	554 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	555
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	556 1, 1.0, 1e-4
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	557 "String"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	558
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	559 - arithmetic operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	560
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	561 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	562
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	563 +,*,-,/
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	564
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	565 - comparison operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	566
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	567 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	568
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	569 == (same as =), >, >=, <=, <, !=
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	570
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	571 - regex operators "~" and its negation "!~"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	572
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	573 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	574
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	575 INFO/HAYSTACK ~ "needle"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	576
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	577 - parentheses
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	578
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	579 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	580
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	581 (, )
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	582
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	583 - logical operators
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	584
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	585 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	586
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	587 && (same as &), \|\|, \|
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	588
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	589 - INFO tags, FORMAT tags, column names
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	590
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	591 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	592
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	593 INFO/DP or DP
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	594 FORMAT/DV, FMT/DV, or DV
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	595 FILTER, QUAL, ID, REF, ALT[0]
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	596
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	597 - 1 (or 0) to test the presence (or absence) of a flag
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	598
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	599 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	600
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	601 FlagA=1 && FlagB=0
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	602
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	603 - "." to test missing values
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	604
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	605 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	606
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	607 DP=".", DP!=".", ALT="."
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	608
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	609 - missing genotypes can be matched regardless of phase and ploidy (".\|.", "./.", ".") using this expression
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	610
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	611 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	612
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	613 GT="."
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	614
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	615 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	616
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	617 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	618
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	619 TYPE="indel" \| TYPE="snp"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	620
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	621 - array subscripts, "*" for any field
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	622
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	623 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	624
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	625 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	626 DP4[*] == 0
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	627 CSQ[] ~ "missense_variant.deleterious"
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	628
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	629 - function on FORMAT tags (over samples) and INFO tags (over vector fields)
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	630
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	631 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	632
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	633 MAX, MIN, AVG, SUM, STRLEN, ABS
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	634
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	635 - 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
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	636
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	637 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	638
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	639 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	640
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	641 Notes:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	642
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	643 - String comparisons and regular expressions are case-insensitive
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	644 - If the subscript "*" is used in regular expression search, the whole field
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	645 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	646 true for the string vector INFO/STR=AB,CD.
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	647 - Variables and function names are case-insensitive, but not tag names. For
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	648 example, "qual" can be used instead of "QUAL", "strlen()" instead of
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	649 "STRLEN()" , but not "dp" instead of "DP".
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	650
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	651 Examples:
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	652
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	653 ::
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	654
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	655 MIN(DV)>5
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	656 MIN(DV/DP)>0.3
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	657 MIN(DP)>10 & MIN(DV)>3
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	658 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	659 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	660 QUAL>10 \| FMT/GQ>10 .. selects only GQ>10 samples
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	661 QUAL>10 \|\| FMT/GQ>10 .. selects all samples at QUAL>10 sites
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	662 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2)
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	663 MIN(DP)>35 && AVG(GQ)>50
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	664 ID=@file .. selects lines with ID present in the file
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	665 ID!=@~/file .. skip lines with ID present in the ~/file
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	666 MAF[0]<0.05 .. select rare variants at 5% cutoff
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	667
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	668 ]]></token>
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	669
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	670
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	671
8959eda17fca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643 iuc parents: 0 diff changeset	672
0 a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b iuc parents: diff changeset	673 </macros>

Mercurial > repos > iuc > bcftools_call

annotate macros.xml @ 3:5337db17a5f7 draft