Mercurial > repos > iuc > stacks_ustacks
annotate stacks_ustacks.xml @ 0:7c5004f8cd49 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
author | iuc |
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date | Tue, 14 Jun 2016 14:06:23 -0400 |
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children | 216c469422d2 |
rev | line source |
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0
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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1 <tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0"> |
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
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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> |
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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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6 <expand macro="requirements"/> |
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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="stdio"/> |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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8 <command><![CDATA[ |
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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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9 #from os.path import splitext |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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10 #import re |
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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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11 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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12 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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13 |
7c5004f8cd49
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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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 #if $sample.ext == "fastqsanger": |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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17 #set $data_path = splitext($sample.name)[0] |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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18 #set $data_path = re.sub(r'\.1$', '', $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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19 #set $data_path = "stacks_inputs/" + $data_path + ".fq" |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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20 #set inputype = "fastq" |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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21 #else: |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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22 #set $data_path = splitext($sample.name)[0] |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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23 #set $data_path = re.sub(r'\.1$', '', $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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24 #set $data_path = "stacks_inputs/" + $data_path + ".fa" |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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25 #set inputype = "fasta" |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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26 #end if |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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27 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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28 ln -s "${sample}" "${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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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 |
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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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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 |
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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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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 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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41 -i $sample_id |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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42 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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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
iuc
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44 -M $M |
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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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45 $R |
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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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46 $H |
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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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47 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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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 f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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49 $assembly_options.r |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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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
iuc
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51 --max_locus_stacks $assembly_options.max_locus_stacks |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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52 #if str($assembly_options.k_len): |
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
iuc
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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
iuc
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55 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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56 #if $gapped.use_gapped: |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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57 --gapped |
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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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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 |
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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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61 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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62 ## snp_model |
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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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63 #if str( $snp_options.select_model.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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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
iuc
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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
iuc
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67 --alpha $snp_options.select_model.alpha |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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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
iuc
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69 --model_type snp |
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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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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
iuc
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71 #else |
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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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72 --model_type fixed |
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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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73 --bc_err_freq $bc_err_freq |
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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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74 #end if |
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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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75 |
7c5004f8cd49
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 f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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77 ]]></command> |
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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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78 |
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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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79 <inputs> |
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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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80 <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" /> |
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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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81 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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82 <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/> |
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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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83 |
7c5004f8cd49
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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84 <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/> |
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85 <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> |
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86 <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" /> |
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87 <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" /> |
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88 |
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89 <section name="assembly_options" title="SNP Model Options (ustacks options)" expanded="True"> |
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90 <param name="r" argument="-r" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Enable the Removal algorithm, to drop highly-repetitive stacks (and nearby errors) from the algorithm" /> |
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91 <param name="d" argument="-d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Enable the Deleveraging algorithm, used for resolving over merged tags" /> |
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92 <param name="max_locus_stacks" argument="--max_locus_stacks" type="integer" value="3" label="Maximum number of stacks at a single de novo locus"/> |
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93 <param name="k_len" 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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94 </section> |
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95 |
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96 <conditional name="gapped"> |
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97 <param name="use_gapped" argument="--gapped" type="boolean" checked="false" label="Perform gapped alignments between stacks" /> |
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98 <when value="false"></when> |
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99 <when value="true"> |
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100 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/> |
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101 <param name="min_aln_len" 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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102 </when> |
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103 </conditional> |
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104 |
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105 <!-- SNP Model options --> |
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106 <section name="snp_options" title="SNP Model Options (ustacks options)" expanded="False"> |
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107 <expand macro="snp_options_full"/> |
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108 </section> |
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109 </inputs> |
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110 |
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111 <outputs> |
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112 <collection name="tabs" type="list" label="Stacks from ${on_string}"> |
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113 <discover_datasets pattern="(?P<name>.+\.tags)\.tsv" ext="tabular" directory="stacks_outputs" /> |
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114 <discover_datasets pattern="(?P<name>.+\.snps)\.tsv" ext="tabular" directory="stacks_outputs" />> |
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115 <discover_datasets pattern="(?P<name>.+\.alleles)\.tsv" ext="tabular" directory="stacks_outputs" /> |
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116 <discover_datasets pattern="(?P<name>.+\.models)\.tsv" ext="tabular" directory="stacks_outputs" /> |
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117 </collection> |
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118 </outputs> |
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119 |
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120 <tests> |
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121 <test> |
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122 <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" /> |
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123 <param name="sample_id" value="4" /> |
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124 |
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125 <output_collection name="tabs"> |
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126 <element name="PopA_01.tags"> |
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127 <assert_contents> |
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128 <has_text text="generated on " /> |
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129 </assert_contents> |
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130 </element> |
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131 <element name="PopA_01.snps"> |
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132 <assert_contents> |
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133 <has_text text="generated on " /> |
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134 </assert_contents> |
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135 </element> |
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136 <element name="PopA_01.alleles"> |
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137 <assert_contents> |
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138 <has_text text="generated on " /> |
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139 </assert_contents> |
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140 </element> |
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141 <element name="PopA_01.models"> |
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142 <assert_contents> |
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143 <has_text text="generated on " /> |
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144 </assert_contents> |
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145 </element> |
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146 </output_collection> |
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147 </test> |
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148 </tests> |
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149 |
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150 <help> |
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151 <![CDATA[ |
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152 .. class:: infomark |
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153 |
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154 **What it does** |
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155 |
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156 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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157 |
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158 -------- |
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159 |
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160 **Input files** |
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161 |
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162 FASTQ, FASTA |
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163 |
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164 **Output files** |
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165 |
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166 - XXX.tags.tsv file: |
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167 |
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168 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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169 |
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170 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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171 |
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172 |
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173 - XXX.snps.tsv file: |
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174 |
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175 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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176 |
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177 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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178 |
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179 |
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180 - XXX.alleles.tsv file: |
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181 |
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182 See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_ |
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183 |
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184 @STACKS_INFOS@ |
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185 ]]> |
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186 </help> |
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187 <expand macro="citation" /> |
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188 </tool> |
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189 |