Mercurial > repos > iuc > stacks_clonefilter

annotate stacks_clonefilter.xml @ 5:87cbcd4038f4 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 21:52:36 +0000
parents 40a90780ac77
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
parents:
diff changeset
1 <tool id="stacks_clonefilter" name="Stacks: clone filter" version="@WRAPPER_VERSION@.0">
4
40a90780ac77 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 5f2ec13ecca435abaac2b99ba21f1d6497ec7139"
iuc
parents: 2
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2 <description>Identify PCR clones</description>
0
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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3 <macros>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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4 <import>macros.xml</import>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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5 </macros>
5
87cbcd4038f4 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"/>
0
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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7 <expand macro="requirements"/>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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8 <expand macro="stdio"/>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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9 <command><![CDATA[
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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10
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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11 #if $data_type.dt_select == "single"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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13 #if $data_type.fname.is_of_type('fastqsanger')
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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14 #set $ext = ".fq"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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15 #set inputype = "fastq"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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16 #else
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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17 #set $ext = ".fq.gz"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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18 #set inputype = "gzfastq"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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19 #end if
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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21 ln -s '$data_type.fname' R1$ext &&
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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22 #else
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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24 #if $data_type.fwd.is_of_type('fastqsanger')
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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25 #set $ext = ".fq"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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26 #set inputype = "fastq"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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27 #else
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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28 #set $ext = ".fq.gz"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
parents:
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29 #set inputype = "gzfastq"
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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30 #end if
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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31
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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32 ln -s '$data_type.fwd' R1$ext &&
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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33 ln -s '$data_type.rev' R2$ext &&
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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34 #end if
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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35
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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37 mkdir clone_outputs
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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38
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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39 &&
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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41 clone_filter
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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42 #if $data_type.dt_select == 'single':
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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43 -f R1$ext
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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44
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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45 #else
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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46 -1 R1$ext
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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47 -2 R2$ext
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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48 #end if
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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49
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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50 -i $inputype
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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51
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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52 -o clone_outputs
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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53
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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54
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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55 #if $oligo_len_1
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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56 --oligo_len_1 $oligo_len_1
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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57 $data_type.barcode_encoding
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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58 #end if
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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59 #if $oligo_len_2
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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60 --oligo_len_2 $oligo_len_2
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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61 #end if
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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62
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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63 -y gzfastq
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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64
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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65 ]]></command>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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66 <inputs>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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67 <conditional name="data_type">
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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68 <param name="dt_select" type="select" label="Single or Paired-end">
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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69 <option value="single">Single</option>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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70 <option value="pair">Pair</option>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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71 </param>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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72 <when value="single">
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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73 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" />
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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74 <param name="barcode_encoding" type="select" label="Barcode location">
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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75 <expand macro="barcode_encoding_single" />
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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76 </param>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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77
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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78 </when>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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79 <when value="pair">
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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80 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" />
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
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81 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" />
2
596b1e36b13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit d127e451bbe9267768092f1d890ab1a147c3b2cf
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parents: 1
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82 <param name="barcode_encoding" type="select" label="Barcode location">
596b1e36b13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit d127e451bbe9267768092f1d890ab1a147c3b2cf
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parents: 1
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83 <expand macro="barcode_encoding_pair" />
0
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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84 </param>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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85 </when>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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86 </conditional>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
parents:
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87 <param name="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
parents:
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88 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
iuc
parents:
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89
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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90 </inputs>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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91 <outputs>
1
0d6bc3ce9b6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 2a75760c2be67944c6d980eca7bbdc7ab4f90486
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parents: 0
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92 <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz">
0
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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93 <filter>data_type['dt_select'] == 'single'</filter>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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94 </data>
0806ba804d4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
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95
5
87cbcd4038f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
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96 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string}: forward">
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97 <filter>data_type['dt_select'] == 'pair'</filter>
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98 </data>
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99 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string}: reverse">
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100 <filter>data_type['dt_select'] == 'pair'</filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <test>
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105 <conditional name="data_type">
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106 <param name="dt_select" value="single" />
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107 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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108 </conditional>
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109 <param name="oligo_len_1" value="6" />
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110 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
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111 </test>
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112 <test>
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113 <conditional name="data_type">
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114 <param name="dt_select" value="single" />
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115 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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116 </conditional>
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117 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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118 </test>
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119 <test>
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120 <conditional name="data_type">
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121 <param name="dt_select" value="pair" />
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122 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" />
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123 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" />
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124 </conditional>
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125 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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126 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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127 </test>
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128 <test>
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129 <conditional name="data_type">
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130 <param name="dt_select" value="pair" />
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131 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
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132 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" />
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133 </conditional>
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134 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
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135 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
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136 </test>
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137 </tests>
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138 <help>
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139 <![CDATA[
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140 .. class:: infomark
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141
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142
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143 The clone_filter program is designed to identify PCR clones.
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144
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145 @STACKS_INFOS@
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146 ]]>
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147 </help>
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148 <expand macro="citation" />
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149 </tool>