Mercurial > repos > iuc > stacks2_shortreads

annotate macros_process.xml @ 6:97575d01f06b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
author iuc
date Wed, 11 May 2022 06:48:08 +0000
parents 4e280b27a831
children
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ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <?xml version="1.0"?>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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3 <!-- macros and tokens for process_radtags and process_short_reads -->
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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4
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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5 <macros>
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6
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7
0
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8 <token name="@PROCESS_IOOPTIONS@"><![CDATA[
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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9 -p stacks_inputs/
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10 #if $input_type.input_type_select == "paired"
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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11 --paired
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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13 -i $inputype
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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14 $input_type.barcode_encoding
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15 #if $input_type.barcode_encoding != ''
4e280b27a831 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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16 -b '$input_type.barcode'
4e280b27a831 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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17 #end if
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18 #if str( $outype ) != "auto"
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19 -y $outype
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20 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 -o stacks_outputs
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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22 ]]></token>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 <xml name="process_output_types">
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24 <param name="outype" argument="-y" type="select" label="Output format" >
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25 <option value="auto" selected="True">Same as input</option>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 <option value="fastq">fastq</option>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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27 <option value="fasta">fasta</option>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28 <option value="gzfastq">gzipped fastq</option>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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29 <option value="gzfasta">gzipped fasta</option>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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30 </param>
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31 </xml>
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33 <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34 <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>
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35 <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/"/>
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36 <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/"/>
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37 </xml>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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38 <xml name="discover_faq_output_macro" token_pattern="" token_dir="">
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39 <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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40 <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/>
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41 </xml>
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42
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43 <xml name="process_outputs">
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44 <yield/>
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45 <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">
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46 <filter>input_type['input_type_select'] == "paired"</filter>
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47 <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/>
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48 </collection>
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49 <!-- note irrespective of -y output is always named fastq and are never zipped -->
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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50 <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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51 <filter>capture is True and input_type['input_type_select'] == "single"</filter>
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52 <expand macro="discover_faq_output_macro" pattern="(?P&lt;name&gt;.*)" dir="stacks_outputs/discarded"/>
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53 </collection>
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54 <collection name="discarded_paired" type="list:paired" label="${tool.name} on ${on_string} Discarded reads">
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55 <filter>capture is True and input_type['input_type_select'] == "paired"</filter>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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56 <expand macro="discover_faq_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/discarded"/>
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57 </collection>
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58 </xml>
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59
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60 <!-- FASTQ filtering options -->
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61 <xml name="process_filter">
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62 <conditional name="filter_cond" >
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63 <param name="filter_select" type="select" label="Do quality filtering">
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64 <option value="yes">Yes</option>
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65 <option value="no" selected="true">No</option>
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66 </param>
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67 <when value="yes">
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68 <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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69 <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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70 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/>
0
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71 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
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72 <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/>
0
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73 </when>
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74 <when value="no">
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75 <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="Useful if your data has already been trimmed"/>
0
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76 </when>
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77 </conditional>
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78 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
0
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79 </xml>
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80 <token name="@PROCESS_FILTER@"><![CDATA[
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81 #if $filter_cond.filter_select == 'yes':
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82 -w $filter_cond.sliding
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83 -s $filter_cond.score
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84 $filter_cond.remove
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85 $filter_cond.discard
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86 $filter_cond.filter_illumina
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87 #else
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88 #if str($filter_cond.len_limit) != "":
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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89 --len_limit $filter_cond.len_limit
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90 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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91 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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92 $capture
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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93 ]]></token>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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94 <token name="@PROCESS_FASTQ_POSTPROC@"><![CDATA[
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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95 #if $capture:
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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96 && mkdir stacks_outputs/discarded/
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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97 && mv stacks_outputs/*discards stacks_outputs/discarded/
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98
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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99 ## fix the _R[12]_0 that was added for preparing the input
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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100 #if $input_type.input_type_select == 'paired':
2
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101 && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done)
0
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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102 #end if
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103 ## also remove the gz which is added by procrad (but its uncompressed)
2
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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104 && (find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done)
0
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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105
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106 ## the discard files are named fastq even if the output is fasta
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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107 #if str($outype).endswith("fasta"):
2
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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108 && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done)
0
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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109 #else
2
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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110 && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done)
0
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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111 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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112 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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113 ## prepare paired read output for processing in galaxy
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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114 #if $input_type.input_type_select == 'paired':
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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115 && mkdir stacks_outputs/remaining
2
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116 && (find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done)
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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117 && (find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done)
0
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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118 #end if
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119 ]]></token>
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120
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121 <!-- adapter trimming options -->
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122 <xml name="process_adapter">
2
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123 <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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124 <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read"/>
0
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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125 <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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126 </xml>
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127 <token name="@PROCESS_ADAPTER@"><![CDATA[
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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128 ## Adapter options
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129 #if str($options_advanced.adapter_1) != "":
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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130 --adapter_1 $options_advanced.adapter_1
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131 #end if
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132 #if str($options_advanced.adapter_2) != "":
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133 --adapter_2 $options_advanced.adapter_2
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134 #end if
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135 #if str($options_advanced.adapter_mm) != "":
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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136 --adapter_mm $options_advanced.adapter_mm
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137 #end if
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138 ]]></token>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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139
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140 <!-- barcode rescue options -->
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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141 <xml name="rescue_barcode">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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142 <conditional name="rescue_cond">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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143 <param name="rescue" type="select" argument="-r" label="Rescue mutated barcodes and RAD-Tags?">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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144 <option value="-r">yes</option>
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145 <option value="" selected="true">no</option>
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146 </param>
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147 <when value="-r">
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148 <param argument="--barcode_dist_1" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing first read barcodes" help="(default 1)"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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149 <param argument="--barcode_dist_2" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing paired read barcodes" help="(default value for single end barcodes)"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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150 </when>
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151 <when value=""/>
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152 </conditional>
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153 </xml>
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154 <token name="@RESCUE_BARCODE@"><![CDATA[
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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155 #if str($options_advanced.rescue_cond.rescue) != ""
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156 $options_advanced.rescue_cond.rescue
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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157 #if str($options_advanced.rescue_cond.barcode_dist_1) != "":
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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158 --barcode_dist_1 $options_advanced.rescue_cond.barcode_dist_1
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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159 #end if
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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160 #if str($options_advanced.rescue_cond.barcode_dist_2) != "":
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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161 --barcode_dist_2 $options_advanced.rescue_cond.barcode_dist_2
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162 #end if
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163 #end if
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164 ]]></token>
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165
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166 <!-- advanced options that are shared -->
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167 <xml name="common_advanced">
2
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168 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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169 <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output"/>
0
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170 </xml>
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171 <token name="@COMMON_ADVANCED@"><![CDATA[
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172 #if str($options_advanced.truncate)
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173 -t $options_advanced.truncate
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174 #end if
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175 $options_advanced.retain_header
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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176 ]]></token>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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177 </macros>
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43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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