Mercurial > repos > iuc > bcftools_plugin_fixploidy
annotate macros.xml @ 14:068e100f634a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
author | iuc |
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date | Sat, 15 Jan 2022 13:33:05 +0000 |
parents | d9f9294ccccc |
children | f2482aa4862e |
rev | line source |
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0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 <macros> |
11
ceb03be4f31b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
iuc
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2 <token name="@TOOL_VERSION@">1.10</token> |
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d9f9294ccccc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
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3 <xml name="bio_tools"> |
d9f9294ccccc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
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4 <xrefs> |
d9f9294ccccc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
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5 <xref type="bio.tools">bcftools</xref> |
d9f9294ccccc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
parents:
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6 </xrefs> |
d9f9294ccccc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
parents:
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diff
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7 </xml> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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8 <xml name="requirements"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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9 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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diff
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10 <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement> |
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ceb03be4f31b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
iuc
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11 <requirement type="package" version="1.10">htslib</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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12 <yield /> |
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7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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13 </requirements> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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14 </xml> |
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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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15 <xml name="samtools_requirement"> |
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ceb03be4f31b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
iuc
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16 <requirement type="package" version="1.10">samtools</requirement> |
5
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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17 </xml> |
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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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18 <xml name="matplotlib_requirement"> |
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d9f9294ccccc
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
parents:
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diff
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19 <requirement type="package" version="3.4.3">matplotlib</requirement> |
8
2978f7d1f150
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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20 </xml> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff
changeset
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21 <xml name="version_command"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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22 <version_command>bcftools 2>&1 | grep 'Version:'</version_command> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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23 </xml> |
3
f6a06fcdebdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
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24 |
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7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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25 <xml name="citations"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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26 <citations> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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27 <citation type="doi">10.1093/bioinformatics/btp352</citation> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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28 <yield /> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
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29 </citations> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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30 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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31 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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32 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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33 <token name="@THREADS@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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34 --threads \${GALAXY_SLOTS:-4} |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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35 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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36 <token name="@PREPARE_ENV@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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37 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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38 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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39 ]]> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
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40 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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41 <xml name="macro_input"> |
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12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf" label="VCF/BCF Data" /> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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43 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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44 <token name="@PREPARE_INPUT_FILE@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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45 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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46 ## May need to symlink input if there is an associated |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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47 #set $input_vcf = 'input.vcf.gz' |
3
f6a06fcdebdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
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48 #if $input_file.is_of_type('vcf') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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49 bgzip -c '$input_file' > $input_vcf && |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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50 bcftools index $input_vcf && |
3
f6a06fcdebdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
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51 #elif $input_file.is_of_type('vcf_bgzip') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3
iuc
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52 ln -s '$input_file' $input_vcf && |
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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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53 #if $input_file.metadata.tabix_index: |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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54 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi && |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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55 #else |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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56 bcftools index $input_vcf && |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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57 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
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58 #elif $input_file.is_of_type('bcf') |
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7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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59 #set $input_vcf = 'input.bcf' |
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b7dc6f8084ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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60 ln -s '$input_file' $input_vcf && |
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7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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61 #if $input_file.metadata.bcf_index: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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62 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
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63 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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64 bcftools index $input_vcf && |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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65 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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66 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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67 ]]> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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68 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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69 <token name="@INPUT_FILE@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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70 $input_vcf |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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71 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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72 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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73 <xml name="macro_inputs"> |
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12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
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74 <param name="input_files" type="data" format="vcf,vcf_bgzip,bcf" label="Other VCF/BCF Datasets" multiple="True" /> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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75 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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76 <token name="@PREPARE_INPUT_FILES@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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77 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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78 ## May need to symlink input if there is an associated |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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79 #set $input_vcfs = [] |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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80 #set $vcfs_list_file = 'vcfs_list' |
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81 #for (i, input_file) in enumerate($input_files): |
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82 #set $input_vcf = 'input' + str($i) + '.vcf.gz' |
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83 #if $input_file.is_of_type('vcf') |
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84 bgzip -c '$input_file' > $input_vcf && |
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85 bcftools index $input_vcf && |
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86 #elif $input_file.is_of_type('vcf_bgzip') |
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87 ln -s '$input_file' $input_vcf && |
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88 #if $input_file.metadata.tabix_index: |
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89 ln -s '${input_file.metadata.tabix_index}' ${input_vcf}.tbi && |
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90 #else |
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91 bcftools index $input_vcf && |
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92 #end if |
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93 #elif $input_file.is_of_type('bcf') |
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94 #set $input_vcf = 'input' + str($i) + '.bcf.gz' |
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95 ln -s '$input_file' $input_vcf && |
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96 #if $input_file.metadata.bcf_index: |
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97 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && |
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98 #else |
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99 bcftools index $input_vcf && |
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100 #end if |
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101 #end if |
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102 echo '$input_vcf' >> $vcfs_list_file && |
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103 $input_vcfs.append($input_vcf) |
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104 #end for |
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105 ]]> |
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106 </token> |
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107 <token name="@INPUT_FILES@"> |
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108 #echo ' '.join($input_vcfs)# |
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109 </token> |
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110 <token name="@INPUT_LIST_FILE@"> |
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111 $vcfs_list_file |
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112 </token> |
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113 |
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114 <xml name="test_using_reference" token_select_from="history" token_ref=""> |
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115 <conditional name="reference_source"> |
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116 <param name="reference_source_selector" value="@SELECT_FROM@" /> |
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117 <param name="fasta_ref" ftype="fasta" value="@REF@" /> |
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118 </conditional> |
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119 </xml> |
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120 |
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121 <xml name="macro_fasta_ref"> |
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122 <conditional name="reference_source"> |
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123 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> |
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124 <option value="cached">Use a built-in genome</option> |
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125 <option value="history">Use a genome from the history</option> |
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126 </param> |
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127 <when value="cached"> |
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128 <param name="fasta_ref" type="select" label="Reference genome"> |
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129 <options from_data_table="fasta_indexes"> |
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130 <filter type="data_meta" column="dbkey" key="dbkey" ref="input_file" /> |
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131 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" /> |
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132 </options> |
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133 </param> |
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134 </when> |
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135 <when value="history"> |
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136 <param name="fasta_ref" type="data" format="fasta" label="Reference genome" /> |
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137 </when> |
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138 </conditional> |
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139 </xml> |
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140 <token name="@PREPARE_FASTA_REF@"> |
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141 <![CDATA[ |
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142 #set $input_fa_ref = None |
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143 #if 'fasta_ref' in $section and $section.fasta_ref: |
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144 #if 'reference_source_selector' in $section: |
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145 #if str($section.reference_source_selector) == "history": |
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146 #set $input_fa_ref = 'ref.fa' |
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147 ln -s '$section.fasta_ref' $input_fa_ref && |
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148 samtools faidx $input_fa_ref && |
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149 #else: |
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150 #set $input_fa_ref = str($section.fasta_ref.fields.path) |
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151 #end if |
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152 #end if |
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153 #end if |
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154 ]]> |
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155 </token> |
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156 <token name="@FASTA_REF@"> |
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157 #if $input_fa_ref is not None: |
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158 --fasta-ref $input_fa_ref |
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159 #elif 'fasta_ref' in $section and $section.fasta_ref: |
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160 --fasta-ref '${section.fasta_ref}' |
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161 #end if |
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162 </token> |
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163 |
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164 <xml name="macro_AF_file"> |
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165 <param name="AF_file" argument="--AF-file" type="data" format="tabular" optional="true" label="Allele frequencies file" help="Tab-delimited file containing the columns CHR,POS,REF,ALT,AF" /> |
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166 </xml> |
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167 <!-- This may need to bgzip and tabix the file --> |
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168 <token name="@PREPARE_AF_FILE@"> |
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169 <![CDATA[ |
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170 #if 'AF_file' in $section and $section.AF_file: |
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171 #pass |
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172 #end if |
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173 ]]> |
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174 </token> |
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175 <token name="@AF_FILE@"> |
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176 #if 'AF_file' in $section and $section.AF_file: |
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177 --AF-file '${section.AF_file}' |
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178 #end if |
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179 </token> |
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180 |
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181 <xml name="macro_estimate_AF"> |
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182 <param name="estimate_AF" argument="--estimate-AF" type="data" format="data" optional="true" label="Estimate allele frequency" help="Calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> |
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183 </xml> |
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184 <token name="@ESTIMATE_AF@"> |
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185 #if 'estimate_AF' in $section and $section.estimate_AF: |
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186 --estimate-AF "${section.estimate_AF}" |
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187 #end if |
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188 </token> |
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189 |
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190 <xml name="macro_exons_file"> |
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191 <param name="exons_file" type="data" format="tabular" optional="true" label="Exons file" help="Tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" /> |
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192 </xml> |
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193 <token name="@PREPARE_EXONS_FILE@"> |
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194 <![CDATA[ |
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195 #set $exons_path = None |
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196 #if 'exons_file' in $section and $section.exons_file: |
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197 #set $exons_path = 'exons_file.tab.gz' |
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198 bgzip -c "$section.exons_file" > $exons_path && |
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199 tabix -s 1 -b 2 -e 3 $exons_path && |
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200 #end if |
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201 ]]> |
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202 </token> |
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203 <token name="@EXONS_FILE@"> |
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204 #if 'exons_file' in $section and $section.exons_file: |
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205 --exons $exons_path |
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206 #end if |
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207 </token> |
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208 |
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209 <xml name="macro_ploidy_file"> |
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210 <param name="ploidy_file" type="data" format="tabular" optional="true" label="Ploidy file" help="Tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> |
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211 </xml> |
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212 <token name="@PLOIDY_FILE@"> |
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213 #if 'ploidy_file' in $section and $section.ploidy_file: |
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214 --ploidy "${section.ploidy_file}" |
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215 #end if |
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216 </token> |
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217 |
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218 <xml name="macro_collapse_opt_none"> |
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219 <option value="none">none - require the exact same set of alleles in all files</option> |
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220 </xml> |
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221 <xml name="macro_collapse_opt_id"> |
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222 <option value="id">id - only records with identical ID column are compatible. </option> |
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223 </xml> |
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224 <xml name="macro_collapse"> |
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225 <param name="collapse" type="select" optional="true" label="Collapse" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files"> |
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226 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option> |
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227 <option value="indels">indels - allow different alleles, as long as they all are indels</option> |
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228 <option value="both">both - indels and snps </option> |
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229 <option value="some">some - at least some of the ALTs must match</option> |
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230 <option value="any">any - any combination of alleles</option> |
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231 <yield/> |
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232 </param> |
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233 </xml> |
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234 <token name="@COLLAPSE@"> |
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235 #if $section.collapse: |
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236 --collapse ${section.collapse} |
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237 #end if |
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238 </token> |
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239 |
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240 <xml name="macro_apply_filters"> |
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241 <param argument="--apply_filters" type="text" value="" optional="true" label="Apply filters" |
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242 help="Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")"> |
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243 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator> |
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244 </param> |
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245 </xml> |
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246 <token name="@APPLY_FILTERS@"> |
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247 #if $section.apply_filters: |
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248 --apply-filters '${section.apply_filters}' |
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249 #end if |
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250 </token> |
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251 |
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252 <xml name="macro_select_output_type"> |
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253 <param name="output_type" type="select"> |
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254 <option value="b">compressed BCF</option> |
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255 <!-- no galaxy datatypes for these |
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256 <option value="u">uncompressed BCF</option> |
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257 <option value="z">compressed VCF</option> |
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258 --> |
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259 <option value="v">uncompressed VCF</option> |
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260 </param> |
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261 </xml> |
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262 <token name="@OUTPUT_TYPE@"> |
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263 #if str($output_type) != "__none__": |
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264 --output-type '${output_type}' |
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265 #end if |
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266 </token> |
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267 |
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268 <xml name="macro_vcf_output"> |
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269 <data name="output_file" format="vcf"> |
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270 <change_format> |
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271 <when input="output_type" value="b" format="bcf" /> |
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272 <when input="output_type" value="u" format="bcf" /> |
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273 <when input="output_type" value="z" format="vcf_bgzip" /> |
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274 <when input="output_type" value="v" format="vcf" /> |
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275 </change_format> |
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276 </data> |
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277 </xml> |
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278 |
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279 <xml name="macro_invert_targets"> |
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280 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" |
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281 label="Invert Targets" |
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282 help="inverts the query/filtering applied by the targets" /> |
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283 </xml> |
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284 |
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285 <xml name="macro_restriction_spec" token_type="region" token_label_type="Region"> |
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286 <repeat name="@TYPE@s" title="@LABEL_TYPE@ Filter" default="1" min="1"> |
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287 <param name="chrom" type="text" label="@LABEL_TYPE@ chromosome"> |
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288 <validator type="expression" message="A chromosome identifier is required when specifying a @LABEL_TYPE@ filter">value.strip()</validator> |
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289 </param> |
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290 <param name="start" type="text" label="@LABEL_TYPE@ start position"> |
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291 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> |
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292 </param> |
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293 <param name="stop" type="text" label="@LABEL_TYPE@ end position"> |
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294 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator> |
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295 </param> |
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296 <yield /> |
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297 </repeat> |
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298 </xml> |
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299 |
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300 <xml name="macro_restrictions_file" token_type="region" token_label_type="Region"> |
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301 <param name="@TYPE@s_file" type="data" format="tabular" label="@LABEL_TYPE@s File" help="restrict to @LABEL_TYPE@s listed in a file" /> |
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302 </xml> |
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303 |
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304 <xml name="macro_restrict" token_type="region" token_label_type="Region" > |
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305 <conditional name="@TYPE@s"> |
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306 <param name="@TYPE@s_src" type="select" label="@LABEL_TYPE@s"> |
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307 <option value="__none__">Do not restrict to @LABEL_TYPE@s</option> |
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308 <option value="@TYPE@s">Specify one or more @LABEL_TYPE@(s) directly</option> |
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309 <option value="@TYPE@s_file">Operate on @LABEL_TYPE@s specified in a history dataset</option> |
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310 </param> |
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311 <when value="__none__"/> |
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312 <when value="@TYPE@s"> |
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313 <expand macro="macro_restriction_spec" type="@TYPE@" label_type="@LABEL_TYPE@" /> |
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314 <yield /> |
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315 </when> |
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316 <when value="@TYPE@s_file"> |
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317 <expand macro="macro_restrictions_file" type="@TYPE@" label_type="@LABEL_TYPE@" /> |
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318 <yield /> |
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319 </when> |
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320 </conditional> |
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321 </xml> |
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322 |
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323 <token name="@PARSE_INTERVALS@"> |
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324 <![CDATA[ |
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diff
changeset
|
325 #set $components = [] |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
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326 #for $i in $intervals: |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
|
327 #set $chrom = str($i.chrom).strip() |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
|
328 #set $start = str($i.start).strip() |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
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329 #set $stop = str($i.stop).strip() |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
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330 #if $start or $stop: |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
|
331 $components.append($chrom + ':' + ($start or '0') + '-' + $stop) |
2978f7d1f150
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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332 #else: |
2978f7d1f150
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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333 $components.append($chrom) |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
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334 #end if |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
|
335 #end for |
2978f7d1f150
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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336 #set $intervals_spec = ','.join($components) |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
|
337 ]]> |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
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338 </token> |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
|
339 |
2978f7d1f150
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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340 <token name="@REGIONS@"> |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
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341 <![CDATA[ |
2978f7d1f150
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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342 #if $section.regions.regions_src == 'regions': |
2978f7d1f150
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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343 #set $intervals = $section.regions.regions |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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344 @PARSE_INTERVALS@ |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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345 --regions '$intervals_spec' |
2978f7d1f150
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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346 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: |
2978f7d1f150
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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347 #if $regions_path is not None: |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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348 --regions-file '$regions_path' |
2978f7d1f150
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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349 #else: |
2978f7d1f150
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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350 --regions-file '$section.regions.regions_file' |
2978f7d1f150
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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351 #end if |
2978f7d1f150
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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352 #end if |
2978f7d1f150
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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353 ]]> |
2978f7d1f150
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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354 </token> |
2978f7d1f150
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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355 |
2978f7d1f150
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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356 <token name="@TARGETS@"> |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
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357 <![CDATA[ |
2978f7d1f150
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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358 #if $targets_path: |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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359 --targets-file "${section.targets.invert_targets_file}${targets_path}" |
2978f7d1f150
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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360 #elif $section.targets.targets_src == 'targets': |
2978f7d1f150
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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361 #set $intervals = $section.targets.targets |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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362 @PARSE_INTERVALS@ |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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363 --targets '${section.targets.invert_targets_file}$intervals_spec' |
2978f7d1f150
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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364 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: |
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
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diff
changeset
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365 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" |
2978f7d1f150
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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366 #end if |
2978f7d1f150
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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367 ]]> |
2978f7d1f150
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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368 </token> |
2978f7d1f150
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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369 |
5
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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370 <token name="@PREPARE_REGIONS_FILE@"> |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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371 <![CDATA[ |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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372 #set $regions_path = None |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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373 #if 'regions' in $section |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
4
diff
changeset
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374 #if $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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375 #if $section.regions.regions_file.ext.startswith('bed'): |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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diff
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376 #set $regions_path = 'regions_file.bed' |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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377 ln -s '$section.regions.regions_file' $regions_path && |
aec8cc772e0c
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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378 #end if |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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379 #end if |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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380 #end if |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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381 ]]> |
aec8cc772e0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
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diff
changeset
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382 </token> |
8
2978f7d1f150
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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383 |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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384 <token name="@PREPARE_TARGETS_FILE@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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changeset
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385 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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diff
changeset
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386 #set $targets_path = None |
3
f6a06fcdebdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents:
2
diff
changeset
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387 #if 'targets' in $section |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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388 #if $section.targets.targets_src == 'targets_file': |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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389 #set $targets_path = 'targets_file.tab.gz' |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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390 bgzip -c "$section.targets.targets_file" > $targets_path && |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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391 tabix -s 1 -b 2 -e 2 $targets_path && |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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392 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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393 #elif $tgts_sec.targets_file: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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394 #set $targets_path = 'targets_file.tab.gz' |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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395 bgzip -c "$section.targets_file" > $targets_path && |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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396 tabix -s 1 -b 2 -e 2 $targets_path && |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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397 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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398 ]]> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
399 </token> |
8
2978f7d1f150
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents:
7
diff
changeset
|
400 |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
401 <token name="@TARGETS_FILE@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
402 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
403 #if $targets_path is not None: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
404 --targets-file "${section.invert_targets_file}${targets_path}" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
405 #elif $section.targets_file: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
406 --targets-file "${section.invert_targets_file}${section.targets_file}" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
407 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
408 ]]> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
409 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
410 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
411 <xml name="macro_samples"> |
7
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
412 <param argument="--samples" type="text" value="" optional="true" label="Samples" |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
413 help="Comma separated list of samples to annotate (or exclude)"> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
414 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
415 </param> |
3
f6a06fcdebdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents:
2
diff
changeset
|
416 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" |
7
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
417 help="Inverts the query/filtering applied by Samples (adds "^" prefix to exclude)" /> |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
418 <param argument="--samples_file" type="data" format="tabular" optional="true" label="Samples file" |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
419 help="File of samples to include" /> |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
420 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples file" |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
421 help="inverts the query/filtering applied by Samples file" /> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
422 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
423 <token name="@SAMPLES@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
424 #set $samples_defined = False |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
425 #if str($section.samples) != '': |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
426 #set $samples_defined = True |
4
b7dc6f8084ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents:
3
diff
changeset
|
427 --samples '${section.invert_samples}${section.samples}' |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
428 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
429 #if $section.samples_file: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
430 #set $samples_defined = True |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
431 --samples-file "${section.invert_samples_file}${section.samples_file}" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
432 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
433 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
434 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
435 <xml name="macro_sample"> |
7
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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diff
changeset
|
436 <param name="sample" type="text" optional="true" label="Sample" help="Apply variants of the given sample" /> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
437 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
438 <token name="@SAMPLE@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
439 #if $section.sample: |
4
b7dc6f8084ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
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diff
changeset
|
440 --sample '${section.sample}' |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
441 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
442 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
443 |
12
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
444 <xml name="macro_include_exclude_validate_sanitize"> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
445 <validator type="expression" message="Single quote or trailing backslash not allowed">"'" not in value and value[-1] != "\\"</validator> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
446 <sanitizer> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
447 <valid initial="string.ascii_letters,string.digits,string.whitespace,string.punctuation"> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
448 <remove value="@" /> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
449 <remove value="'" /> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
450 </valid> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
451 </sanitizer> |
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
452 </xml> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
453 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
454 <xml name="macro_include"> |
7
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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diff
changeset
|
455 <param argument="--include" type="text" optional="true" label="Include" help="Select sites for which the expression is true"> |
12
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
456 <expand macro="macro_include_exclude_validate_sanitize" /> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
457 </param> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
458 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
459 <token name="@INCLUDE@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
460 #if $section.include: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
461 --include '${section.include}' |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
462 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
463 </token> |
12
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
464 |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
465 <xml name="macro_exclude"> |
7
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
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diff
changeset
|
466 <param argument="--exclude" type="text" optional="true" label="Exclude" help="Exclude sites for which the expression is true"> |
12
365325116147
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8ad854180e3be0934cdb1f0021886199a2edf9c3"
iuc
parents:
11
diff
changeset
|
467 <expand macro="macro_include_exclude_validate_sanitize" /> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
468 </param> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
469 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
470 <token name="@EXCLUDE@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
471 #if $section.exclude: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
472 --exclude '${section.exclude}' |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
473 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
474 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
475 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
476 <xml name="macro_columns"> |
7
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
477 <param name="columns" type="text" value="" optional="true" label="Columns" |
12152af85697
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents:
6
diff
changeset
|
478 help="List of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
479 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
480 </param> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
481 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
482 <token name="@COLUMNS@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
483 #if $section.columns != '': |
4
b7dc6f8084ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents:
3
diff
changeset
|
484 --columns '${section.columns}' |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
485 #end if |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
486 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
487 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
488 <xml name="macro_haploid2diploid"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
489 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" /> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
490 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
491 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
492 <xml name="macro_vcf_ids"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
493 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" /> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
494 </xml> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
495 <token name="@VCF_IDS@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
496 ${section.vcf_ids} |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
497 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
498 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
499 <token name="@OUTPUT_HELP@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
500 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
501 Output Type |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
502 ----------- |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
503 |
3
f6a06fcdebdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
iuc
parents:
2
diff
changeset
|
504 Output compressed BCF (b), or uncompressed VCF (v). |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
505 Use the BCF option when piping between bcftools subcommands to speed up |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
506 performance by removing unecessary compression/decompression |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
507 and VCF<->BCF conversion. |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
508 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
509 This Galaxy tool recommends using the compressed BCF format |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
510 as piping is not implemented, and uncompressed data would |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
511 use unnecessary amounts of space. |
4
b7dc6f8084ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents:
3
diff
changeset
|
512 ]]></token> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
513 <token name="@REGIONS_HELP@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
514 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
515 Region Selections |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
516 ----------------- |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
517 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
518 Regions can be specified in a VCF, |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
519 BED, or tab-delimited file (the default). The columns of the |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
520 tab-delimited file are: CHROM, POS, and, optionally, POS_TO, |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
521 where positions are 1-based and inclusive. Uncompressed |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
522 files are stored in memory, while bgzip-compressed and |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
523 tabix-indexed region files are streamed. Note that sequence |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
524 names must match exactly, "chr20" is not the same as "20". |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
525 Also note that chromosome ordering in FILE will be |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
526 respected, the VCF will be processed in the order in which |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
527 chromosomes first appear in FILE. However, within |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
528 chromosomes, the VCF will always be processed in ascending |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
529 genomic coordinate order no matter what order they appear in |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
530 FILE. Note that overlapping regions in FILE can result in |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
531 duplicated out of order positions in the output. This option |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
532 requires indexed VCF/BCF files. |
4
b7dc6f8084ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
iuc
parents:
3
diff
changeset
|
533 ]]></token> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
534 <token name="@TARGETS_HELP@"><![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
535 Targets |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
536 ------- |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
537 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
538 Similar to regions, but the next position is accessed by streaming the whole |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
539 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
540 applied simultaneously: regions uses the index to jump to a region and targets discards |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
541 positions which are not in the targets. Unlike regions, targets can be prefixed with |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
542 "^" to request logical complement. For example, "^X,Y,MT" indicates that |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
543 sequences X, Y and MT should be skipped. Yet another difference between the two |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
544 is that regions checks both start and end positions of indels, whereas targets checks |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
545 start positions only. |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
546 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
547 For the bcftools call command, with the option -C alleles, third column of the |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
548 targets file must be comma-separated list of alleles, starting with the |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
549 reference allele. Note that the file must be compressed and index. Such a file |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
550 can be easily created from a VCF using:: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
551 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
552 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
553 ]]> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
554 <!-- TODO: galaxy-ify --> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
555 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
556 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
557 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
558 <token name="@COLLAPSE_HELP@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
559 Collapse |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
560 -------- |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
561 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
562 Controls how to treat records with duplicate positions and defines compatible |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
563 records across multiple input files. Here by "compatible" we mean records which |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
564 should be considered as identical by the tools. For example, when performing |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
565 line intersections, the desire may be to consider as identical all sites with |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
566 matching positions (bcftools isec -c all), or only sites with matching variant |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
567 type (bcftools isec -c snps -c indels), or only sites with all alleles |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
568 identical (bcftools isec -c none). |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
569 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
570 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
571 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
572 | Flag value | Result | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
573 +============+================================================================+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
574 | none | only records with identical REF and ALT alleles are compatible | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
575 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
576 | some | only records where some subset of ALT alleles match are | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
577 | | compatible | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
578 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
579 | all | all records are compatible, regardless of whether the ALT | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
580 | | alleles match or not. In the case of records with the same | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
581 | | position, only the first wil lbe considered and appear on | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
582 | | output. | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
583 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
584 | snps | any SNP records are compatible, regardless of whether the ALT | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
585 | | alleles match or not. For duplicate positions, only the first | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
586 | | SNP record will be considered and appear on output. | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
587 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
588 | indels | all indel records are compatible, regardless of whether the | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
589 | | REF and ALT alleles match or not. For duplicate positions, | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
590 | | only the first indel record will be considered and appear on | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
591 | | output. | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
592 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
593 | both | abbreviation of "-c indels -c snps" | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
594 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
595 | id | only records with identical ID column are compatible. | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
596 | | Supportedby bcftools merge only. | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
597 +------------+----------------------------------------------------------------+ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
598 </token> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
599 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
600 <token name="@EXPRESSIONS_HELP@"> |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
601 <![CDATA[ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
602 Expressions |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
603 ----------- |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
604 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
605 Valid expressions may contain: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
606 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
607 - numerical constants, string constants |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
608 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
609 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
610 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
611 1, 1.0, 1e-4 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
612 "String" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
613 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
614 - arithmetic operators |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
615 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
616 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
617 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
618 +,*,-,/ |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
619 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
620 - comparison operators |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
621 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
622 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
623 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
624 == (same as =), >, >=, <=, <, != |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
625 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
626 - regex operators "~" and its negation "!~" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
627 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
628 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
629 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
630 INFO/HAYSTACK ~ "needle" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
631 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
632 - parentheses |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
633 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
634 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
635 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
636 (, ) |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
637 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
638 - logical operators |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
639 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
640 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
641 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
642 && (same as &), ||, | |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
643 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
644 - INFO tags, FORMAT tags, column names |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
645 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
646 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
647 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
648 INFO/DP or DP |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
649 FORMAT/DV, FMT/DV, or DV |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
650 FILTER, QUAL, ID, REF, ALT[0] |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
651 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
652 - 1 (or 0) to test the presence (or absence) of a flag |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
653 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
654 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
655 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
656 FlagA=1 && FlagB=0 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
657 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
658 - "." to test missing values |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
659 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
660 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
661 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
662 DP=".", DP!=".", ALT="." |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
663 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
664 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
|
665 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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666 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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changeset
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667 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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668 GT="." |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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changeset
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669 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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changeset
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670 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other) |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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changeset
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671 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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672 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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673 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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674 TYPE="indel" | TYPE="snp" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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675 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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676 - array subscripts, "*" for any field |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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677 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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678 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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679 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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680 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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681 DP4[*] == 0 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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682 CSQ[*] ~ "missense_variant.*deleterious" |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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683 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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684 - function on FORMAT tags (over samples) and INFO tags (over vector fields) |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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685 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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686 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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687 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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688 MAX, MIN, AVG, SUM, STRLEN, ABS |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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689 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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690 - variables calculated on the fly if not present: number of alternate alleles; number of samples; count of alternate alleles; minor allele count (similar to AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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691 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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692 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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|
693 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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694 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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695 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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696 **Notes:** |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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697 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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698 - String comparisons and regular expressions are case-insensitive |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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699 - If the subscript "*" is used in regular expression search, the whole field |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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700 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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701 true for the string vector INFO/STR=AB,CD. |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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702 - Variables and function names are case-insensitive, but not tag names. For |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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703 example, "qual" can be used instead of "QUAL", "strlen()" instead of |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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704 "STRLEN()" , but not "dp" instead of "DP". |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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705 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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706 **Examples:** |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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707 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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708 :: |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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709 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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710 MIN(DV)>5 |
7d6599c7e2fb
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711 MIN(DV/DP)>0.3 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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712 MIN(DP)>10 & MIN(DV)>3 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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713 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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714 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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715 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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716 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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717 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2) |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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718 MIN(DP)>35 && AVG(GQ)>50 |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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719 ID=@file .. selects lines with ID present in the file |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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720 ID!=@~/file .. skip lines with ID present in the ~/file |
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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721 MAF[0]<0.05 .. select rare variants at 5% cutoff |
4
b7dc6f8084ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 3edcac645f34d5a94884dedaf95c5774f4afc5c7
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diff
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722 ]]></token> |
0
7d6599c7e2fb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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723 </macros> |