Mercurial > repos > iuc > stacks_ustacks
annotate stacks_ustacks.xml @ 12:4cce81af50a8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author | iuc |
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date | Fri, 07 Apr 2023 22:04:41 +0000 |
parents | a4ec4f620a77 |
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rev | line source |
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4
ff04b3748654
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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1 <tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0"> |
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7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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2 <description>align short reads into stacks</description> |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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3 <macros> |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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4 <import>macros.xml</import> |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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5 </macros> |
12
4cce81af50a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
iuc
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6 <expand macro="bio_tools"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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7 <expand macro="requirements"/> |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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8 <expand macro="stdio"/> |
7c5004f8cd49
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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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10 |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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11 @CLEAN_EXT@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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12 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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13 mkdir stacks_inputs stacks_outputs |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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14 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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15 && |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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16 |
8
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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17 #if $sample.is_of_type('fastqsanger') |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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18 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fq" |
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7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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19 #set inputype = "fastq" |
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bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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20 #else if $sample.is_of_type('fastqsanger.gz') |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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21 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fq.gz" |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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22 #set inputype = "gzfastq" |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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23 #else |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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24 #set $data_path = "stacks_inputs/" + $clean_ext($sample.element_identifier) + ".fa" |
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7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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25 #set inputype = "fasta" |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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26 #end if |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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27 |
8
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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28 ln -s '${sample}' '${data_path}' |
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7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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29 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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30 && |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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31 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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32 ustacks |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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33 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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34 -p \${GALAXY_SLOTS:-1} |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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35 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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36 -f $data_path |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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37 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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38 -t $inputype |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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39 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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40 ## Batch description |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
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41 -i 1 |
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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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42 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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43 -m $m |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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44 -M $M |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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45 $R |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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46 $H |
7c5004f8cd49
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 f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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48 ## Assembly |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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49 $assembly_options.keep_high_cov |
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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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50 $assembly_options.d |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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51 --max_locus_stacks $assembly_options.max_locus_stacks |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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52 #if str($assembly_options.k_len) |
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7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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53 --k_len $assembly_options.k_len |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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54 #end if |
7c5004f8cd49
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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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56 #if $gapped.use_gapped == "yes" |
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7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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57 --gapped |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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58 --max_gaps $gapped.max_gaps |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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59 --min_aln_len $gapped.min_aln_len |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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60 #end if |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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61 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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62 ## snp_model |
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63 #if str( $snp_options.select_model.model_type) == "bounded" |
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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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64 --model_type bounded |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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65 --bound_low $snp_options.select_model.bound_low |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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66 --bound_high $snp_options.select_model.bound_high |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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67 --alpha $snp_options.select_model.alpha |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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68 #else if str( $snp_options.select_model.model_type) == "snp" |
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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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69 --model_type snp |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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70 --alpha $snp_options.select_model.alpha |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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71 #else |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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72 --model_type fixed |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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73 --bc_err_freq $bc_err_freq |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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74 #end if |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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75 |
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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 -o stacks_outputs |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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77 |
8
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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78 2>&1 | tee ustacks.log |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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79 |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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80 ## If input is in gz format, stacks will output gzipped files (no option to control this) |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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81 #if $sample.is_of_type('fastqsanger.gz') |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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82 && gunzip stacks_outputs/*.gz |
bdad4fb6f85a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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83 #end if |
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84 |
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85 && |
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86 |
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87 stacks_summary.py --stacks-prog ustacks --res-dir stacks_outputs --logfile ustacks.log --summary stacks_outputs/summary.html |
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88 ]]></command> |
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89 |
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90 <inputs> |
8
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91 <param name="sample" argument="-f" format="fastqsanger,fastqsanger.gz,fasta" type="data" label="Input short reads from an individual" /> |
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92 |
12
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93 <param argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/> |
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94 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> |
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95 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" /> |
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96 <param argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> |
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97 |
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98 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True"> |
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99 <param argument="--keep_high_cov" type="boolean" checked="false" truevalue="--keep-high-cov" falsevalue="" label="Disable the algorithm that removes highly-repetitive stacks and nearby errors. " /> |
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100 <param argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" /> |
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101 <param argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/> |
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102 <param argument="--k_len" type="integer" value="" optional="true" label="K-mer size for matching between alleles and loci (automatically calculated by default)"/> |
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103 </section> |
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104 |
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105 <conditional name="gapped"> |
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106 <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks"> |
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107 <option value="no" selected="true">No</option> |
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108 <option value="yes">Yes</option> |
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109 </param> |
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110 <when value="no"/> |
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111 <when value="yes"> |
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112 <param argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/> |
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113 <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/> |
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114 </when> |
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115 </conditional> |
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116 |
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117 <!-- SNP Model options --> |
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118 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False"> |
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119 <expand macro="snp_options_full"/> |
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120 </section> |
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121 </inputs> |
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122 |
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123 <outputs> |
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124 <data format="txt" name="output_log" label="ustacks.log with ${tool.name} on ${on_string}" from_work_dir="ustacks.log" /> |
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125 |
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126 <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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127 |
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128 <collection name="tabs" type="list" label="Stacks from ${on_string}"> |
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129 <discover_datasets pattern="(?P<name>.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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130 <discover_datasets pattern="(?P<name>.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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131 <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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132 <discover_datasets pattern="(?P<name>.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" /> |
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133 </collection> |
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134 </outputs> |
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135 |
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136 <tests> |
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137 <test> |
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138 <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> |
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139 |
3
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140 <output name="output_log"> |
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141 <assert_contents> |
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142 <has_text text="done." /> |
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143 </assert_contents> |
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144 </output> |
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145 <output name="output_summary"> |
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146 <assert_contents> |
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147 <has_text text="Stacks Statistics" /> |
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148 </assert_contents> |
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149 </output> |
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150 |
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151 <output_collection name="tabs"> |
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152 <element name="PopA_01.tags"> |
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153 <assert_contents> |
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154 <has_text text="generated on " /> |
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155 </assert_contents> |
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156 </element> |
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157 <element name="PopA_01.snps"> |
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158 <assert_contents> |
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159 <has_text text="generated on " /> |
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160 </assert_contents> |
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161 </element> |
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162 <element name="PopA_01.alleles"> |
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163 <assert_contents> |
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164 <has_text text="generated on " /> |
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165 </assert_contents> |
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166 </element> |
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167 <element name="PopA_01.models"> |
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168 <assert_contents> |
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169 <has_text text="generated on " /> |
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170 </assert_contents> |
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171 </element> |
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172 </output_collection> |
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173 </test> |
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174 <test> |
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175 <param name="sample" value="demultiplexed/PopA_01.1.fq.gzip" ftype="fastqsanger.gz" /> |
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176 |
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177 <output name="output_log"> |
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178 <assert_contents> |
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179 <has_text text="done." /> |
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180 </assert_contents> |
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181 </output> |
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182 <output name="output_summary"> |
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183 <assert_contents> |
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184 <has_text text="Stacks Statistics" /> |
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185 </assert_contents> |
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186 </output> |
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187 |
0
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188 <output_collection name="tabs"> |
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189 <element name="PopA_01.tags"> |
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190 <assert_contents> |
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191 <has_text text="generated on " /> |
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192 </assert_contents> |
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193 </element> |
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194 <element name="PopA_01.snps"> |
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195 <assert_contents> |
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196 <has_text text="generated on " /> |
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197 </assert_contents> |
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198 </element> |
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199 <element name="PopA_01.alleles"> |
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200 <assert_contents> |
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201 <has_text text="generated on " /> |
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202 </assert_contents> |
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203 </element> |
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204 <element name="PopA_01.models"> |
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205 <assert_contents> |
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206 <has_text text="generated on " /> |
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207 </assert_contents> |
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208 </element> |
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209 </output_collection> |
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210 </test> |
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211 </tests> |
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212 |
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213 <help> |
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214 <![CDATA[ |
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215 .. class:: infomark |
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216 |
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217 **What it does** |
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218 |
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219 The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework |
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220 |
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221 -------- |
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222 |
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223 **Input files** |
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224 |
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225 FASTQ, FASTA |
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226 |
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227 **Output files** |
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228 |
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229 - XXX.tags.tsv file: |
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230 |
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231 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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232 |
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233 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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234 |
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235 |
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236 - XXX.snps.tsv file: |
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237 |
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238 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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239 |
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240 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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241 |
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242 |
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243 - XXX.alleles.tsv file: |
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244 |
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245 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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246 |
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247 @STACKS_INFOS@ |
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248 ]]> |
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249 </help> |
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250 <expand macro="citation" /> |
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251 </tool> |