Mercurial > repos > iuc > bcftools_mpileup
annotate bcftools_mpileup.xml @ 9:ce9396ddcb2b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
author | iuc |
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date | Thu, 14 Oct 2021 10:16:46 +0000 |
parents | f65383c7ed49 |
children | 6d7dc9a1bef3 |
rev | line source |
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0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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1 <?xml version='1.0' encoding='utf-8'?> |
7
f65383c7ed49
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
iuc
parents:
4
diff
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> |
9
ce9396ddcb2b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
parents:
7
diff
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4 <expand macro="bio_tools" /> |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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5 <macros> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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6 <token name="@EXECUTABLE@">mpileup</token> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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7 <import>macros.xml</import> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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8 <xml name="bam_flag_options"> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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9 <option value="1">Read is paired</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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10 <option value="2">Read is mapped in a proper pair</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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11 <option value="4">The read is unmapped</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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12 <option value="8">The mate is unmapped</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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13 <option value="16">Read strand</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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14 <option value="32">Mate strand</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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15 <option value="64">Read is the first in a pair</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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16 <option value="128">Read is the second in a pair</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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17 <option value="256">The alignment or this read is not primary</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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18 <option value="512">The read fails platform/vendor quality checks</option> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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19 <option value="1024">The read is a PCR or optical duplicate</option> |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
0
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20 </xml> |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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21 </macros> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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22 <expand macro="requirements"> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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23 <expand macro="samtools_requirement"/> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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24 </expand> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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25 <expand macro="version_command" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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26 <command detect_errors="aggressive"><![CDATA[ |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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27 #import re |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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28 #set bam_list = [] |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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29 #if $input.input_number == 'single': |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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30 #set $input_base = $re.sub('\W','_',$input.input_bam.display_name.replace('.bam','').replace('.cram','')) |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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31 #set $ext = 'bam' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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32 #set $idx_ext = 'bai' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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33 #if $input.input_bam.ext == 'cram': |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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34 #set $ext = 'cram' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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35 #set $idx_ext = 'crai' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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36 #end if |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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37 #set $input_name = $input_base + '.' + $ext |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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38 #silent $bam_list.append($input_name) |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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39 ln -s '${input.input_bam}' ${input_name} && |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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40 #if $input.input_bam.ext == 'bam': |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
0
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41 ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} && |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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42 #else: |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
0
diff
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43 ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} && |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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44 #end if |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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45 #else: |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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46 #for $bam_count, $input_bam in enumerate( $input.input_bams ): |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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47 #set $input_base = $re.sub('\W','_',$input_bam.display_name.replace('.bam','').replace('.cram','')) |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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48 #set $ext = 'bam' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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49 #set $idx_ext = 'bai' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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50 #if $input_bam.ext == 'cram': |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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51 #set $ext = 'cram' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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52 #set $idx_ext = 'crai' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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53 #end if |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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54 #set $input_name = $input_base + '.' + $ext |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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55 #silent $bam_list.append($input_name) |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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56 ln -s '${input_bam}' ${input_name} && |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
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57 ln -s '${input_bam.metadata.bam_index}' ${input_name}.${idx_ext} && |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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58 #end for |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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59 #end if |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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60 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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61 #set $input_fa_ref = None |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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62 #if $reference_source.reference_source_selector == "history": |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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0
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63 #set $input_fa_ref = 'ref.fa' |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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64 ln -s '${reference_source.ref_file}' $input_fa_ref && |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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65 samtools faidx $input_fa_ref && |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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66 #elif $reference_source.reference_source_selector == "cached": |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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67 #set $input_fa_ref = $reference_source.ref_file.fields.path |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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68 #end if |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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69 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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70 #set $section = $sec_restrict |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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71 @PREPARE_REGIONS_FILE@ |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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72 @PREPARE_TARGETS_FILE@ |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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73 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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74 bcftools @EXECUTABLE@ |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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75 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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76 #if $input_fa_ref is not None: |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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77 --fasta-ref '$input_fa_ref' |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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78 #else: |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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79 --non-reference |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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diff
changeset
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80 #end if |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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81 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
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82 ## Indel Calling section |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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83 #set $section = $sec_indel |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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84 #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling': |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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85 --skip-indels |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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86 #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling': |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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87 -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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88 -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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89 -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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90 -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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91 -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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92 --open-prob "${section.perform_indel_calling.open_seq_error_probability}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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93 -F "${section.perform_indel_calling.minimum_gapped_read_fraction}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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94 ${section.perform_indel_calling.gapped_read_per_sample} |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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95 #if len( $section.perform_indel_calling.platform_list_repeat ): |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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96 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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97 #end if |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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98 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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99 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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100 ## Filter section |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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101 #set $section = $sec_filtering |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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102 #if str( $section.filter_by_flags.filter_flags ) == "filter": |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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103 #if $section.filter_by_flags.require_flags: |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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104 --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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105 #end if |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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106 #if $section.filter_by_flags.exclude_flags: |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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107 --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])} |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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108 #end if |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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109 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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110 -d "${section.max_reads_per_bam}" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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111 ${section.skip_anomalous_read_pairs} |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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112 #if str( $section.quality.quality_settings ) == "adjust": |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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113 $section.quality.baq |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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114 -q "${section.quality.minimum_mapping_quality}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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115 -Q "${section.quality.minimum_base_quality}" |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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116 -C "${section.quality.coefficient_for_downgrading}" |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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117 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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118 #if str( $section.read_groups.read_groups_selector ) == "ignore_rg": |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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119 --ignore-RG |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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120 #elif str( $section.read_groups.read_groups_selector ) == "paste": |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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121 -G "${section.read_groups.rg_action}${read_groups_file}" |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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122 #elif str( $section.read_groups.read_groups_selector ) == "history" |
2
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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123 -G "${section.read_groups.rg_action}${section.read_groups.read_groups}" |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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124 #end if |
12f7c5315f7f
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125 |
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126 #set $section = $sec_output_options |
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127 #if $section.output_tags: |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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128 --annotate "$section.output_tags" |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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129 #end if |
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130 #if $section.gvcf: |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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131 --gvcf "$section.gvcf" |
0
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132 #end if |
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133 |
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134 ## Subset section |
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135 #set $section = $sec_subset |
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136 @SAMPLES@ |
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137 |
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138 ## Restrict section |
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139 #set $section = $sec_restrict |
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140 @REGIONS@ |
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141 @TARGETS@ |
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142 |
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143 @THREADS@ |
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144 |
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145 @OUTPUT_TYPE@ |
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146 |
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147 ## Primary Input/Outputs |
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148 #echo ' '.join($bam_list)# |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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149 > '$output_file' |
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150 #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste": |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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151 && echo 'read-groups:' |
cf06b44624c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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152 && cat ${read_groups_file} |
0
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153 #end if |
2
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154 ]]></command> |
0
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155 <configfiles> |
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156 <configfile name="read_groups_file"> |
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157 <![CDATA[#slurp |
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158 #set pasted_data = '' |
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159 #set $section = $sec_filtering |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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160 #if str( $section.read_groups.read_groups_selector ) == "paste": |
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161 #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() ) |
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162 #end if |
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163 #slurp |
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164 ${pasted_data} |
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165 ]]> |
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166 </configfile> |
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167 </configfiles> |
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168 <inputs> |
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169 |
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170 <conditional name="input"> |
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171 <param name="input_number" type="select" label="Alignment Inputs"> |
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172 <option value="single">Single BAM/CRAM</option> |
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173 <option value="multiple">Multiple BAM/CRAMs</option> |
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174 </param> |
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175 <when value="single"> |
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176 <param name="input_bam" type="data" format="bam,cram" label="Input BAM/CRAM" /> |
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177 </when> |
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178 <when value="multiple"> |
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179 <param name="input_bams" type="data" format="bam,cram" multiple="true" label="Input BAM/CRAMs" /> |
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180 </when> |
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181 </conditional> |
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182 |
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183 <conditional name="reference_source"> |
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184 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
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185 <option value="cached">Locally cached</option> |
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186 <option value="history">History</option> |
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187 <option value="none">No Reference</option> |
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188 </param> |
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189 <when value="cached"> |
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190 <param name="ref_file" type="select" label="Select reference genome"> |
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191 <options from_data_table="fasta_indexes"/> |
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192 </param> |
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193 </when> |
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194 <when value="history"> |
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195 <param name="ref_file" type="data" format="fasta" label="Genome Reference" /> |
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196 </when> |
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197 <when value="none"/> |
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198 </conditional> |
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199 |
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200 <section name="sec_indel" expanded="false" title="Indel Calling"> |
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201 <conditional name="perform_indel_calling"> |
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202 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling"> |
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203 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option> |
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204 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option> |
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205 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option> |
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206 </param> |
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207 <when value="perform_indel_calling_def" /> |
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208 <when value="perform_indel_calling"> |
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209 <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> |
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210 <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="--ext-prob; Reducing this value leads to longer indels. default=20"/> |
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211 <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." help="--tandem-qual; default=100"/> |
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212 <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" help="--max-idepth; default=250"/> |
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213 <param name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" label="Minimum gapped reads for indel candidates" help="--min-ireads; default=1"/> |
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214 <param name="open_seq_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> |
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215 <param name="minimum_gapped_read_fraction" type="float" value="0.002" label="Minimum fraction of gapped reads" help="--gap-frac; default=0.002"/> |
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216 <param name="gapped_read_per_sample" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/> |
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217 <repeat name="platform_list_repeat" title="Platform for INDEL candidates"> |
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218 <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/> |
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219 </repeat> |
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220 </when> |
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221 <when value="do_not_perform_indel_calling" /> |
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222 </conditional> |
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223 </section> |
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224 |
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225 <section name="sec_filtering" expanded="false" title="Input Filtering Options"> |
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226 <param name="max_reads_per_bam" type="integer" value="250" max="1024" min="1" label="Max reads per BAM" help="--max-depth; default=250"/> |
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227 <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/> |
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228 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/> |
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229 <conditional name="filter_by_flags"> |
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230 <param name="filter_flags" type="select" label="Set filter by flags"> |
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231 <option selected="True" value="nofilter">Do not filter</option> |
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232 <option value="filter">Filter by flags to exclude or require</option> |
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233 </param> |
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234 <when value="filter"> |
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235 <param name="require_flags" type="select" display="checkboxes" label="Require" multiple="True" help="--incl-flags"> |
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236 <expand macro="bam_flag_options" /> |
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237 </param> |
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238 <param name="exclude_flags" type="select" display="checkboxes" label="Exclude" multiple="True" help="--excl-flags"> |
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239 <expand macro="bam_flag_options" /> |
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240 </param> |
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241 </when> |
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242 <when value="nofilter" /> |
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243 </conditional> |
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244 <conditional name="quality"> |
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245 <param label="Quality Options" name="quality_settings" type="select"> |
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246 <option value="none" selected="True">defaults</option> |
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247 <option value="adjust">Set base and mapping quality options</option> |
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248 </param> |
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249 <when value="adjust"> |
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250 <param name="baq" type="select" label="per-Base Alignment Quality"> |
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251 <help> |
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252 --no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments. |
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253 --redo-BAQ; ignore existing BQ tags |
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254 </help> |
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255 <option value="">Default</option> |
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256 <option value="--no-BAQ">disable BAQ (per-Base Alignment Quality) (no-BAQ)</option> |
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257 <option value="--redo-BAQ">recalculate BAQ on the fly, ignore existing BQs (redo-BAQ)</option> |
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258 </param> |
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259 <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/> |
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260 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/> |
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261 <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" help="--min-BQ; default=13"/> |
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262 </when> |
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263 <when value="none"/> |
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264 </conditional> |
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265 |
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266 <conditional name="read_groups"> |
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267 <param name="read_groups_selector" type="select" label="Select read groups to include or exclude" help="--read-groups"> |
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268 <option value="no_limit" selected="True">use defaults</option> |
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269 <option value="history">From an uploaded text file</option> |
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270 <option value="paste">Paste a list of read groups</option> |
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271 <option value="ignore_rg">Ignore RG tags. Treat all reads in one alignment file as one sample. </option> |
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272 </param> |
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273 <when value="history"> |
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274 <param name="read_groups" format="txt" label="Text file" type="data"> |
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275 <validator type="dataset_ok_validator" /> |
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276 </param> |
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277 <param name="rg_action" type="select" label="Include or Exclude these Read Groups"> |
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278 <option value="" selected="true">Include</option> |
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279 <option value="^">Exclude</option> |
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280 </param> |
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281 </when> |
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282 <when value="paste"> |
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283 <param name="group_paste" type="text" size="10x35" area="true" label="Read groups" help="Paste a list of read groups" /> |
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284 <param name="rg_action" type="select" label="Include or Exclude these Read Groups"> |
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285 <option value="" selected="true">Include</option> |
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286 <option value="^">Exclude</option> |
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287 </param> |
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288 </when> |
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289 <when value="ignore_rg" /> |
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290 <when value="no_limit" /> |
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291 </conditional> |
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292 </section> |
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293 |
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294 <section name="sec_restrict" expanded="false" title="Restrict to"> |
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295 <expand macro="macro_restrict" /> |
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296 <expand macro="macro_restrict" type="target" label_type="Target"> |
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297 <expand macro="macro_invert_targets" /> |
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298 </expand> |
0
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299 </section> |
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300 <section name="sec_subset" expanded="false" title="Subset Options"> |
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301 <expand macro="macro_samples" /> |
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302 </section> |
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303 |
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304 <section name="sec_output_options" expanded="false" title="Output options"> |
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305 <param name="output_tags" optional="True" type="select" multiple="True" display="checkboxes" label="Optional tags to output" help="--output-tags"> |
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306 <option value="DP">DP (Number of high-quality bases)</option> |
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307 <option value="AD">AD (Allelic depth)</option> |
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308 <option value="ADF">ADF (Allelic depth on the forward strand)</option> |
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309 <option value="ADR">ADR (Allelic depth on the reverse strand)</option> |
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310 <option value="INFO/AD">INFO/AD (Allelic depth)</option> |
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311 <option value="INFO/ADF">INFO/ADF (Allelic depth on the forward strand)</option> |
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312 <option value="INFO/ADR">INFO/ADR (Allelic depth on the reverse strand)</option> |
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313 <option value="SP">SP (Phred-scaled strand bias P-value)</option> |
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314 <option value="DV">DV (Number of high-quality non-reference bases)</option> |
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315 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option> |
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316 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option> |
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317 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option> |
12f7c5315f7f
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318 </param> |
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319 <param name="gvcf" type="text" value="" label="gVCF blocks of homozygous REF calls"> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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320 <help> |
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321 output gVCF blocks of homozygous REF calls, with depth (DP) ranges specified by the list of integers. For example, passing 5,15 will group sites into two types of gVCF blocks, the first with minimum per-sample DP from the interval [5,15) and the latter with minimum depth 15 or more. In this example, sites with minimum per-sample depth less than 5 will be printed as separate records, outside of gVCF blocks. |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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322 </help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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323 <validator type="regex" message="integers separated by commas">^(\d+(,\d+)*)?$</validator> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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324 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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325 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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326 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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327 <expand macro="macro_select_output_type" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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328 |
12f7c5315f7f
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329 </inputs> |
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330 <outputs> |
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331 <expand macro="macro_vcf_output" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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332 </outputs> |
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333 <tests> |
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334 <test> |
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335 <param name="input_number" value="single" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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336 <param name="input_bam" ftype="bam" value="mpileup.1.bam" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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337 <param name="reference_source_selector" value="history" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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338 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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339 <param name="output_type" value="v" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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340 <output name="output_file"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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341 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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342 <has_text text="mpileup" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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343 <has_text text="HG00100" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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344 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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345 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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346 </assert_contents> |
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347 </output> |
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348 </test> |
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349 <test> |
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350 <param name="input_number" value="single" /> |
3
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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351 <param name="input_bam" ftype="bam" value="mpileup.1.bam" /> |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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352 <param name="reference_source_selector" value="cached" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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353 <param name="ref_file" value="mpileup" /> |
3
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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354 <param name="quality_settings" value="adjust" /> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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355 <param name="output_type" value="v" /> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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356 <output name="output_file"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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357 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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358 <has_text text="mpileup" /> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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359 <has_text text="HG00100" /> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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360 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" /> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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361 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" /> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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362 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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363 </output> |
4e1d23e5c691
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364 </test> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
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365 <test> |
4e1d23e5c691
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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366 <param name="input_number" value="single" /> |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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367 <param name="input_bam" ftype="cram" value="mpileup.3.cram" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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368 <param name="reference_source_selector" value="history" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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369 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> |
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370 <param name="output_type" value="v" /> |
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371 <output name="output_file"> |
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372 <assert_contents> |
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373 <has_text text="mpileup" /> |
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374 <has_text text="HG00102" /> |
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375 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=5;" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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376 </assert_contents> |
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377 </output> |
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378 </test> |
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379 <test> |
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380 <param name="input_number" value="multiple" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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381 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> |
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382 <param name="reference_source_selector" value="history" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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383 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> |
4
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384 <section name="sec_restrict"> |
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385 <conditional name="regions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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386 <param name="regions_src" value="regions" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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387 <repeat name="regions"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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388 <param name="chrom" value="17" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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389 <param name="start" value="100" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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390 <param name="stop" value="110" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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391 </repeat> |
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iuc
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392 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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393 </section> |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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394 <param name="output_tags" value="DP,INFO/AD,DV" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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395 <param name="output_type" value="v" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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396 <output name="output_file"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
397 <assert_contents> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
398 <has_text text="mpileup" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
399 <has_text text="HG00100" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
400 <has_text text="HG00101" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
401 <has_text text="HG00102" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
402 <has_text text="ID=DP," /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
403 <not_has_text text="17\t111" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
404 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
405 </assert_contents> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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406 </output> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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407 </test> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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408 <test> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
|
409 <param name="input_number" value="multiple" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
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410 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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411 <param name="reference_source_selector" value="history" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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412 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> |
4
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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3
diff
changeset
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413 <section name="sec_restrict"> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
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414 <conditional name="targets"> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
3
diff
changeset
|
415 <param name="targets_src" value="targets" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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416 <repeat name="targets"> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
3
diff
changeset
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417 <param name="chrom" value="17" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
3
diff
changeset
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418 <param name="start" value="100" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
3
diff
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419 <param name="stop" value="104" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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420 </repeat> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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421 </conditional> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
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422 </section> |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
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423 <param name="output_tags" value="DP,INFO/AD,DV" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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424 <param name="output_type" value="v" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
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425 <output name="output_file"> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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426 <assert_contents> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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427 <has_text text="mpileup" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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428 <has_text text="HG00100" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff
changeset
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429 <has_text text="HG00101" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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changeset
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430 <has_text text="HG00102" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
|
431 <has_text text="ID=DP," /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
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432 <not_has_text text="17\t105" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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changeset
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433 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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434 </assert_contents> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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435 </output> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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436 </test> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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437 <test> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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438 <param name="input_number" value="multiple" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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439 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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440 <param name="reference_source_selector" value="history" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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441 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" /> |
4
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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442 <section name="sec_restrict"> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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443 <conditional name="regions"> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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444 <param name="regions_src" value="regions" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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445 <repeat name="regions"> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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446 <param name="chrom" value="17" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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447 <param name="start" value="1050" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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448 <param name="stop" value="1060" /> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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449 </repeat> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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450 </conditional> |
256e65e460b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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451 </section> |
0
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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452 <param name="filter_flags" value="filter" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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453 <param name="exclude_flags" value="4,16" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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454 <param name="output_type" value="v" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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455 <output name="output_file"> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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456 <assert_contents> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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457 <has_text text="mpileup" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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458 <has_text text="HG00100" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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459 <has_text_matching expression="17\t1050\t.\tA\t...\t0\t.\tDP=12;" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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460 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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461 </output> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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462 </test> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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463 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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464 <help><![CDATA[ |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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465 ===================================== |
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466 bcftools @EXECUTABLE@ |
12f7c5315f7f
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467 ===================================== |
12f7c5315f7f
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468 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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469 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby frame-shifting indels which in combination in fact are not frame-shifting. |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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470 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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471 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option). The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask. The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags. By default this is 16, but if more are required, see the --ncsq option. |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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changeset
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472 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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473 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref) and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot), and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported. |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
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474 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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475 By default, the input VCF should be phased. If phase is unknown, or only partially known, the --phase option can be used to indicate how to handle unphased data. Alternatively, haplotype aware calling can be turned off with the --local-csq option. |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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changeset
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476 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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477 If conflicting (overlapping) variants within one haplotype are detected, a warning will be emitted and predictions will be based on only the first variant in the analysis. |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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478 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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479 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are ignored for the prediction analysis. |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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480 |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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481 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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482 @REGIONS_HELP@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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483 @TARGETS_HELP@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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484 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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485 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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486 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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487 @BCFTOOLS_WIKI@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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488 ]]></help> |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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489 <expand macro="citations" /> |
12f7c5315f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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490 </tool> |