Mercurial > repos > iuc > stacks_populations
annotate stacks_populations.xml @ 12:d1fad35bdb4a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2023 22:00:26 +0000 |
| parents | 95286af4139b |
| children |
| rev | line source |
|---|---|
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12
d1fad35bdb4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
iuc
parents:
11
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changeset
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1 <tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.3"> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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2 <description>analyze a population of individual samples ('populations' program)</description> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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3 <macros> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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4 <import>macros.xml</import> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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5 </macros> |
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12
d1fad35bdb4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
iuc
parents:
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6 <expand macro="bio_tools"/> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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7 <expand macro="requirements"/> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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8 <expand macro="stdio"/> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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9 <command><![CDATA[ |
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2ac5c9616748
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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10 #import re |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff
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11 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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12 mkdir stacks_outputs |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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13 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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14 && |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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15 |
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8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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16 #if str($options_usage.input_type) == 'stacks' |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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17 #for $input_file in $options_usage.input_col |
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4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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18 #set $filename = str($input_file.element_identifier) |
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8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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19 #if not $filename.endswith('.tsv') |
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4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
parents:
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20 #set $filename = $filename + ".tsv" |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
parents:
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21 #end if |
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8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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22 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename) |
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12
d1fad35bdb4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
iuc
parents:
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23 cp '${input_file}' 'stacks_outputs/${filename}' && |
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4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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24 #end if |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
parents:
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25 #end for |
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8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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26 #else if str($options_usage.input_type) == 'vcf' |
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12
d1fad35bdb4a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
iuc
parents:
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27 cp '$options_usage.input_vcf' 'stacks_outputs/batch_1.vcf' && |
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4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
parents:
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28 #end if |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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29 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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changeset
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30 populations |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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31 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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32 -t \${GALAXY_SLOTS:-1} |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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33 |
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8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
4
diff
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34 #if str($options_usage.input_type) == 'vcf' |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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35 -V 'stacks_outputs/batch_1.vcf' |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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36 -O stacks_outputs |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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37 #else |
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4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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38 -P stacks_outputs |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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39 -b $advanced_options.batchid |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
parents:
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40 #end if |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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41 |
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8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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42 -M '$options_usage.popmap' |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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43 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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44 ## Data filtering |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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45 $options_filtering.write_single_snp |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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46 $options_filtering.write_random_snp |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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47 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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48 #if str($options_filtering.lnl) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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49 --lnl_lim $options_filtering.lnl |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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50 #end if |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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51 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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52 -r $options_filtering.minperc |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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53 -p $options_filtering.minpop |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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54 -m $options_filtering.mindepth |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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55 |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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56 #if str($options_filtering.max_obs_het) |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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57 --max_obs_het $options_filtering.max_obs_het |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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58 #end if |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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59 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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60 --min_maf $options_filtering.minminor |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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61 #if str( $options_filtering.correction_select.correction ) != "no_corr" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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62 -f $options_filtering.correction_select.correction |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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63 --p_value_cutoff $options_filtering.correction_select.pcutoff |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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64 #end if |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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65 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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66 ## Fstats |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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67 $fstats |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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68 |
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69 #if $options_kernel.kernel != "" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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70 -k |
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95286af4139b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
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71 --sigma $options_kernel.sigma |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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72 #end if |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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73 |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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74 ## Bootstrap resampling options |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
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75 #if $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_all != "" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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76 --bootstrap |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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77 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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78 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_pifis |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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79 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_fst |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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80 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_div |
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81 $bootstrap_resampling.bootstrap_resampling_mode.bootstrap_phist |
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82 #end if |
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83 |
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84 #if str($bootstrap_resampling.bootstrap_reps) |
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85 --bootstrap_reps $bootstrap_resampling.bootstrap_reps |
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86 #end if |
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87 #if $bootstrap_resampling.bootstrap_wl |
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88 --bootstrap_wl '$bootstrap_resampling.bootstrap_wl' |
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89 #end if |
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90 |
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91 ## output section |
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92 $populations_output.ordered_export |
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93 $populations_output.vcf |
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94 $populations_output.vcf_haplotypes |
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95 $populations_output.genepop |
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96 $populations_output.structure |
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97 $populations_output.fasta |
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98 $populations_output.fasta_strict |
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99 $populations_output.hzar |
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100 $populations_output.phase |
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101 $populations_output.fastphase |
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102 $populations_output.beagle |
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103 $populations_output.beagle_phased |
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104 $populations_output.plink |
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105 $populations_output.phylip |
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106 $populations_output.phylip_var |
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107 $populations_output.phylip_var_all |
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108 $populations_output.treemix |
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109 |
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110 #if $populations_output.options_genomic.genomic != '' |
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111 --genomic |
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112 -e $populations_output.options_genomic.enzyme |
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113 #end if |
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114 |
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115 ## output SQL file (as denovo/refmap) and fst/phi components |
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116 -s |
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117 --log_fst_comp |
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118 |
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119 ## Advanced options |
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120 #if $advanced_options.blacklist |
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121 -B '$advanced_options.blacklist' |
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122 #end if |
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123 #if $advanced_options.whitelist |
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124 -W '$advanced_options.whitelist' |
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125 #end if |
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126 |
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127 && |
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128 |
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129 stacks_summary.py --stacks-prog populations --res-dir stacks_outputs --summary stacks_outputs/summary.html --pop-map '$options_usage.popmap' |
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130 ]]></command> |
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131 |
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132 <inputs> |
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133 <conditional name="options_usage"> |
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134 <param name="input_type" type="select" label="Input type" help="select input file type" > |
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135 <option value="stacks">Stacks output</option> |
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136 <option value="vcf">VCF file</option> |
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137 </param> |
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138 <when value="stacks"> |
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139 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" argument="-P" /> |
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140 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" /> |
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141 </when> |
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142 <when value="vcf"> |
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143 <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" /> |
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144 <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" /> |
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145 </when> |
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146 </conditional> |
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147 |
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148 <section name="options_filtering" title="Data filtering options" expanded="true"> |
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149 |
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150 <param name="minperc" argument="-r" type="float" value="0.5" min="0" max="1" label="Minimum percentage of individuals in a population required to process a locus for that population" /> |
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151 <param name="minpop" argument="-p" type="integer" value="2" label="Minimum number of populations a locus must be present in to process a locus" /> |
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152 <param name="mindepth" argument="-m" type="integer" value="1" label="Specify a minimum stack depth required for individuals at a locus" /> |
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153 <param name="minminor" argument="--min_maf" type="float" value="0.25" label="Specify a minimum minor allele frequency required before calculating Fst at a locus (between 0 and 0.5)" /> |
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12
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154 <param argument="--max_obs_het" type="float" value="" min="0" max="1" optional="true" label="Maximum observed heterozygosity required to process a nucleotide site at a locus." /> |
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155 |
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156 <conditional name="correction_select"> |
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157 <param name="correction" type="select" label="Correction type" help="specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'" > |
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158 <option value="no_corr">No correction</option> |
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159 <option value="p_value">p_value</option> |
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160 <option value="bonferroni_win">bonferroni_win</option> |
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161 <option value="bonferroni_gen">bonferroni_gen</option> |
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162 </param> |
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163 <when value="no_corr"/> |
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164 <when value="p_value"> |
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165 <param name="pcutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" /> |
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166 </when> |
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167 <when value="bonferroni_win"> |
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168 <param name="pcutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" /> |
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169 </when> |
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170 <when value="bonferroni_gen"> |
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171 <param name="pcutoff" type="float" value="0.05" label="P-value cutoff" help="required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction" /> |
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172 </when> |
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173 </conditional> |
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174 |
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175 <param name="lnl" type="float" value="" optional="true" argument="--lnl_lim" label="Filter loci with log likelihood values below this threshold" /> |
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176 |
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177 <param argument="--write_single_snp" truevalue="--write_single_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to only the first SNP per locus." /> |
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178 <param argument="--write_random_snp" truevalue="--write_random_snp" falsevalue="" type="boolean" checked="false" label="Restrict data analysis to one random SNP per locus." /> |
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179 </section> |
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180 |
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181 <section name="populations_output" title="Output options" expanded="true"> |
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182 <param argument="--ordered_export" truevalue="--ordered_export" falsevalue="" type="boolean" checked="false" label="If data is reference aligned, exports will be ordered; only a single representative of each overlapping site." /> |
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183 <param argument="--vcf" truevalue="--vcf" falsevalue="" type="boolean" checked="false" label="Output results in Variant Call Format (VCF)" /> |
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184 <param argument="--vcf_haplotypes" truevalue="--vcf_haplotypes" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Variant Call Format (VCF)." /> |
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185 <param argument="--genepop" truevalue="--genepop" falsevalue="" type="boolean" checked="false" label="Output results in GenePop Format" /> |
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186 <param argument="--structure" truevalue="--structure" falsevalue="" type="boolean" checked="false" label="Output results in Structure Format" /> |
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187 <param argument="--fasta" truevalue="--fasta" falsevalue="" type="boolean" checked="false" label="Output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility." /> |
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188 <param argument="--fasta_strict" truevalue="--fasta_strict" falsevalue="" type="boolean" checked="false" label="Output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci." /> |
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189 <param argument="--hzar" truevalue="--hzar" falsevalue="" type="boolean" checked="false" label="Output genotypes in Hybrid Zone Analysis using R (HZAR) format." /> |
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190 <param argument="--phase" truevalue="--phase" falsevalue="" type="boolean" checked="false" label="Output genotypes in PHASE format" /> |
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191 <param argument="--fastphase" truevalue="--fastphase" falsevalue="" type="boolean" checked="false" label="Output genotypes in fastPHASE format" /> |
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192 <param argument="--beagle" truevalue="--beagle" falsevalue="" type="boolean" checked="false" label="Output genotypes in Beagle format" /> |
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193 <param argument="--beagle_phased" truevalue="--beagle_phased" falsevalue="" type="boolean" checked="false" label="Output haplotypes in Beagle format" /> |
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194 <param argument="--plink" truevalue="--plink" falsevalue="" type="boolean" checked="false" label="Output genotypes in PLINK format" /> |
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195 <param argument="--phylip" truevalue="--phylip" falsevalue="" type="boolean" checked="false" label="Output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction" /> |
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196 <param argument="--phylip_var" truevalue="--phylip_var" falsevalue="" type="boolean" checked="false" label="Include variable sites in the phylip output encoded using IUPAC notation." /> |
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197 <param argument="--phylip_var_all" truevalue="--phylip_var_all" falsevalue="" type="boolean" checked="false" label="Include all sequence as well as variable sites in the phylip output encoded using IUPAC notation." /> |
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198 <param argument="--treemix" truevalue="--treemix" falsevalue="" type="boolean" checked="false" label="Output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard)." /> |
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199 |
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200 <conditional name="options_genomic"> |
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201 <param argument="--genomic" type="select" checked="false" label="Output each nucleotide position (fixed or polymorphic) in all population members to a file"> |
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202 <option value="--genomic">Yes</option> |
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203 <option value="">No</option> |
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204 </param> |
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205 <when value="--genomic"> |
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206 <param name="enzyme" argument="-e" type="select" label="Provide the restriction enzyme used" help="required if generating genomic output" > |
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207 <expand macro="enzymes"/> |
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208 </param> |
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209 </when> |
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210 <when value=""/> |
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211 </conditional> |
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212 </section> |
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213 |
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214 <param argument="--fstats" truevalue="--fstats" falsevalue="" type="boolean" checked="false" label="Enable SNP and haplotype-based F statistics" /> |
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215 |
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216 <conditional name="options_kernel"> |
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217 <param name="kernel" type="select" checked="false" label="enable kernel-smoothed FIS, π, and FST calculations"> |
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218 <option value="-k">Yes</option> |
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219 <option value="" selected="true">No</option> |
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220 </param> |
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221 <when value="-k"> |
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222 <param name="sigma" type="integer" value="150" label="Sigma" help="Standard deviation of the kernel smoothing weight distribution (sigma, default 150Kb)" /> |
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223 </when> |
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224 <when value=""/> |
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225 </conditional> |
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226 |
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227 <section name="bootstrap_resampling" title="Bootstrap resampling" expanded="false"> |
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228 <conditional name="bootstrap_resampling_mode"> |
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229 <param name="bootstrap_all" argument="--bootstrap" type="select" label="Enable bootstrap resampling for all smoothed statistics"> |
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230 <option value="--bootstrap">Yes</option> |
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231 <option value="" selected="true">No</option> |
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232 </param> |
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233 <when value="--bootstrap"/> |
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234 <when value=""> |
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235 <param argument="--bootstrap_pifis" type="boolean" checked="false" truevalue="--bootstrap_pifis" falsevalue="" label="Enable boostrap resampling for smoothed SNP-based Pi and Fis calculations" /> |
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236 <param argument="--bootstrap_fst" type="boolean" checked="false" truevalue="--bootstrap_fst" falsevalue="" label="Enable boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs" /> |
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237 <param argument="--bootstrap_div" type="boolean" checked="false" truevalue="--bootstrap_div" falsevalue="" label="Enable boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes" /> |
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238 <param argument="--bootstrap_phist" type="boolean" checked="false" truevalue="--bootstrap_phist" falsevalue="" label="Enable boostrap resampling for smoothed Phi_st calculations based on haplotypes." /> |
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239 </when> |
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240 </conditional> |
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12
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241 <param argument="--bootstrap_reps" type="integer" value="100" optional="true" label="Number of bootstrap resamplings to calculate" /> |
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242 <param argument="--bootstrap_wl" format="txt,tabular" type="data" optional="true" label="Only bootstrap loci contained in this whitelist" /> |
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243 </section> |
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244 |
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245 <!-- Output options --> |
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246 <section name="advanced_options" title="advanced options" expanded="False"> |
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247 <param name="whitelist" argument="-W" format="txt,tabular" type="data" optional="true" label="Specify a file containing Whitelisted markers to include in the export" /> |
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248 <param name="blacklist" argument="-B" format="txt,tabular" type="data" optional="true" label="Specify a file containing Blacklisted markers to be excluded from the export" /> |
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249 |
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250 <param name="batchid" type="integer" value="1" label="Batch ID to examine when exporting from the catalog" help="Only useful if you analyse data that was processed outside galaxy" /> |
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251 </section> |
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252 </inputs> |
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253 <outputs> |
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254 <expand macro="populations_output_full"/> |
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255 |
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256 <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> |
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257 </outputs> |
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258 |
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259 <tests> |
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260 <test> |
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261 <param name="options_usage|input_type" value="stacks" /> |
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262 <param name="options_usage|input_col"> |
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263 <collection type="list"> |
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264 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" /> |
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265 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" /> |
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266 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" /> |
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267 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" /> |
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268 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" /> |
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269 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" /> |
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270 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" /> |
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271 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" /> |
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272 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" /> |
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273 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> |
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274 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> |
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275 </collection> |
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276 </param> |
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277 <param name="options_usage|popmap" ftype="tabular" value="denovo_map/popmap.tsv" /> |
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278 <param name="options_filtering|correction_select|correction" value="p_value" /> |
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279 |
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280 <param name="populations_output|ordered_export" value="true" /> |
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281 <param name="populations_output|vcf" value="true" /> |
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282 <param name="populations_output|vcf_haplotypes" value="true" /> |
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283 <param name="populations_output|genepop" value="true" /> |
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284 <param name="populations_output|structure" value="true" /> |
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285 <param name="populations_output|fasta" value="true" /> |
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286 <param name="populations_output|fasta_strict" value="true" /> |
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287 <param name="populations_output|hzar" value="true" /> |
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288 <param name="populations_output|phase" value="true" /> |
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289 <param name="populations_output|fastphase" value="true" /> |
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290 <param name="populations_output|beagle" value="true" /> |
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291 <param name="populations_output|beagle_phased" value="true" /> |
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292 <param name="populations_output|plink" value="true" /> |
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293 <param name="populations_output|phylip" value="true" /> |
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294 <param name="populations_output|phylip_var" value="true" /> |
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295 <param name="populations_output|phylip_var_all" value="true" /> |
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296 <param name="populations_output|treemix" value="true" /> |
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297 |
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298 <param name="populations_output|options_genomic|genomic" value="false" /> |
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299 <param name="populations_output|options_genomic|enzyme" value="ecoRI" /> |
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300 |
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301 <output name="output_summary"> |
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302 <assert_contents> |
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303 <has_text text="Stacks Statistics" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
4
diff
changeset
|
304 </assert_contents> |
|
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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diff
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|
305 </output> |
|
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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diff
changeset
|
306 |
|
0
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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changeset
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307 <!-- populations --> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
308 <output name="out_haplotypes"> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff
changeset
|
309 <assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
310 <has_text text="PopA_01" /> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
311 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
312 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
313 <output name="out_hapstats"> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
314 <assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff
changeset
|
315 <has_text text="Smoothed Gene Diversity" /> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
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316 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
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317 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
318 <output name="out_populations_log"> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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319 <assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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diff
changeset
|
320 <has_text text="populations version" /> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
|
321 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
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322 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
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323 <output name="out_sumstats_sum"> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
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324 <assert_contents> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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325 <has_text text="Polymorphic Sites" /> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
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326 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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327 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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328 <output name="out_sumstats"> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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329 <assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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330 <has_text text="Smoothed Pi" /> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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331 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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332 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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333 <output name="out_vcf"> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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334 <assert_contents> |
|
4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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diff
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335 <has_text text="fileformat=VCFv4.2" /> |
|
0
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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diff
changeset
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336 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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337 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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338 <output name="out_treemix_pop"> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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339 <assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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340 <has_text text="TreeMix v1.1;" /> |
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c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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341 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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342 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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343 <output name="out_fasta"> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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344 <assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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345 <has_text text="AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC" /> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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346 </assert_contents> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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347 </output> |
|
c1faa67441e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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changeset
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348 </test> |
|
8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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349 <test> |
|
4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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350 <param name="options_usage|input_type" value="vcf" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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351 <param name="options_usage|input_vcf" value="populations/batch_1.vcf" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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352 <param name="options_usage|popmap" ftype="tabular" value="denovo_map/popmap.tsv" /> |
|
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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353 <param name="options_filtering|correction_select|correction" value="p_value" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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354 |
|
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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355 <param name="populations_output|ordered_export" value="true" /> |
|
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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356 <param name="populations_output|vcf" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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357 <param name="populations_output|vcf_haplotypes" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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358 <param name="populations_output|genepop" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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359 <param name="populations_output|structure" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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360 <param name="populations_output|fasta" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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361 <param name="populations_output|fasta_strict" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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362 <param name="populations_output|hzar" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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363 <param name="populations_output|phase" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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364 <param name="populations_output|fastphase" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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365 <param name="populations_output|beagle" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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366 <param name="populations_output|beagle_phased" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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367 <param name="populations_output|plink" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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368 <param name="populations_output|phylip" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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369 <param name="populations_output|phylip_var" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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370 <param name="populations_output|phylip_var_all" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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371 <param name="populations_output|treemix" value="true" /> |
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d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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372 |
|
8
f5115df39480
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iuc
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373 <param name="populations_output|options_genomic|genomic" value="false" /> |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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374 |
|
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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375 <output name="output_summary"> |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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diff
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376 <assert_contents> |
|
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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377 <has_text text="Stacks Statistics" /> |
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f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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diff
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378 </assert_contents> |
|
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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diff
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379 </output> |
|
4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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changeset
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380 |
|
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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381 <!-- populations --> |
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8
f5115df39480
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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382 <output name="out_haplotypes"> |
|
4
d0b325dfe508
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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383 <assert_contents> |
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384 <has_text text="PopA_01" /> |
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385 </assert_contents> |
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386 </output> |
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387 <output name="out_hapstats"> |
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388 <assert_contents> |
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389 <has_text text="Smoothed Gene Diversity" /> |
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390 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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391 </output> |
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392 <output name="out_populations_log"> |
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393 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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394 <has_text text="populations version" /> |
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395 </assert_contents> |
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396 </output> |
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397 <output name="out_sumstats_sum"> |
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398 <assert_contents> |
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399 <has_text text="Polymorphic Sites" /> |
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400 </assert_contents> |
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401 </output> |
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402 <output name="out_sumstats"> |
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403 <assert_contents> |
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404 <has_text text="Smoothed Pi" /> |
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405 </assert_contents> |
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406 </output> |
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407 <output name="out_vcf"> |
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408 <assert_contents> |
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409 <has_text text="fileformat=VCFv4.2" /> |
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410 </assert_contents> |
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411 </output> |
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412 <output name="out_treemix_pop"> |
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413 <assert_contents> |
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414 <has_text text="TreeMix v1.1;" /> |
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415 </assert_contents> |
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416 </output> |
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417 <output name="out_fasta"> |
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418 <assert_contents> |
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8
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419 <has_text text="CLocus_0_Sample_1_Locus_0_Allele_1" /> |
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4
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420 </assert_contents> |
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421 </output> |
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8
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422 </test> |
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423 </tests> |
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424 <help> |
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425 <![CDATA[ |
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426 .. class:: infomark |
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427 |
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428 **What it does** |
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429 |
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430 This program will be executed in place of the genotypes program when a population is being processed through the pipeline. A map specifiying which individuals belong to which population is submitted to the program and the program will then calculate population genetics statistics, expected/observed heterzygosity, π, and FIS at each nucleotide position. The populations program will compare all populations pairwise to compute FST. If a set of data is reference aligned, then a kernel-smoothed FST will also be calculated. |
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431 |
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432 -------- |
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433 |
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434 **Input files** |
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435 |
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436 Output from denovo_map or ref_map |
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437 |
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438 - Population map:: |
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439 |
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440 indv_01 1 |
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441 indv_02 1 |
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442 indv_03 1 |
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443 indv_04 2 |
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444 indv_05 2 |
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445 indv_06 2 |
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446 |
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447 |
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448 **Output files** |
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449 |
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11
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450 - XXX.tags.tsv file: |
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451 |
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452 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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453 |
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454 Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence. |
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455 |
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456 |
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11
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457 - XXX.snps.tsv file: |
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458 |
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459 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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460 |
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461 Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one. |
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462 |
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463 |
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11
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
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464 - XXX.alleles.tsv file: |
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0
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465 |
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466 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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467 |
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468 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
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469 - XXX.matches.tsv file: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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470 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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471 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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472 |
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473 Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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474 |
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475 |
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476 - other files: |
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477 |
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478 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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479 |
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480 @STACKS_INFOS@ |
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481 ]]> |
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482 </help> |
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483 <expand macro="citation" /> |
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484 </tool> |