Mercurial > repos > iuc > bcftools_gtcheck

comparison bcftools_gtcheck.xml @ 3:bf8c3c146a1c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Tue, 31 Jan 2017 12:42:49 -0500
parents 025adf89e10d
children d8c55ac67d89
comparison
equal deleted inserted replaced
2:025adf89e10d 3:bf8c3c146a1c
13 #set $section = $sec_restrict 13 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@ 14 @PREPARE_TARGETS_FILE@
15 #set $section = $sec_default 15 #set $section = $sec_default
16 #set $genotypes_vcf = None 16 #set $genotypes_vcf = None
17 #if $section.genotypes: 17 #if $section.genotypes:
18 #if $section.genotypes.datatype.file_ext == 'vcf' 18 #if $section.genotypes.is_of_type('vcf')
19 #set $genotypes_vcf = 'genotypes.vcf.gz' 19 #set $genotypes_vcf = 'genotypes.vcf.gz'
20 bgzip -c "$section.genotypes" > $genotypes_vcf && 20 bgzip -c "$section.genotypes" > $genotypes_vcf &&
21 bcftools index $genotypes_vcf && 21 bcftools index $genotypes_vcf &&
22 #elif $section.genotypes.datatype.file_ext == 'bcf' 22 #elif $section.genotypes.is_of_type('bcf')
23 #set $genotypes_vcf = 'genotypes.bcf' 23 #set $genotypes_vcf = 'genotypes.bcf'
24 ln -s "$ection.genotypes" $genotypes_vcf && 24 ln -s "$ection.genotypes" $genotypes_vcf &&
25 #if $section.genotypes.metadata.bcf_index: 25 #if $section.genotypes.metadata.bcf_index:
26 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi && 26 ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
27 #else 27 #else
28 bcftools index $genotypes_vcf && 28 bcftools index $genotypes_vcf &&
29 #end if 29 #end if
30 #end if 30 #end if
31 #end if 31 #end if
32 32
78 <section name="sec_restrict" expanded="false" title="Restrict to"> 78 <section name="sec_restrict" expanded="false" title="Restrict to">
79 <expand macro="macro_regions" /> 79 <expand macro="macro_regions" />
80 <expand macro="macro_targets" /> 80 <expand macro="macro_targets" />
81 </section> 81 </section>
82 <section name="sec_default" expanded="true" title="Default Options"> 82 <section name="sec_default" expanded="true" title="Default Options">
83 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" 83 <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
84 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/> 84 help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
85 <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" /> 85 <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
86 <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" /> 86 <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
87 <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" /> 87 <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
88 <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" /> 88 <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />