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1 <tool id="minced" name="detect CRISPR sequences" version="0.1.5">
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2 <description>(minced)</description>
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3 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="250" merge_outputs="output,output_region,output_ggf_full,output_ggf,output_fasta" />
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4 <requirements>
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5 <requirement type="package" version="0.1.5">minced</requirement>
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6 <requirement type="set_environment">MINCED_SCRIPT_PATH</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range=":-1" level="fatal" />
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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12 <command>
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13 temp_output=\$(mktemp);
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14 minced
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15 -minNR $minNR
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16 -minRL $minRL
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17 -maxRL $maxRL
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18 -minSL $minSL
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19 -maxSL $maxSL
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20 #if str($searchWL) != 'none':
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21 -searchWL $searchWL
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22 #end if
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23 $input
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24 \$temp_output
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25 #if '-spacers' in str($outputs).split():
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26 -spacers
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27 #end if
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28 #if '-gffFull' in str($outputs).split():
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29 -gffFull
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30 #end if
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31 #if '-gff' in str($outputs).split():
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32 -gff
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33 #end if
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34 ;
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35
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36 python \$MINCED_SCRIPT_PATH/reformat.py \$temp_output results.bed results.tab;
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37 #if '-spacers' in str($outputs).split():
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38 mv \$temp_output'_spacers.fa' $output_fasta;
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39 #end if
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40 </command>
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41 <inputs>
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42 <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
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43
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44 <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
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45 <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
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46 <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
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47 <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
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48 <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
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49 <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
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50 <option value="none" selected="true">default</option>
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51 <option value="6">6</option>
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52 <option value="7">7</option>
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53 <option value="8">8</option>
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54 <option value="9">9</option>
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55 </param>
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56
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57 <param name="outputs" type="select" multiple="True" label="Additional output format" help="Please select a output format.">
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58 <option value="-gff">summary results in gff format</option>
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59 <option value="BED" selected="true">summary results in BED format</option>
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60 <option value="-gffFull">detailed results in gff format</option>
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61 <option value="TABULAR" selected="true">detailed results in tabular format</option>
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62 <option value="-spacers">fasta formatted file containing the spacers</option>
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63 <validator type="no_options" message="Please select at least one output file." />
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64 </param>
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65
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66 </inputs>
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67 <outputs>
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68 <data format="tabular" name="output" from_work_dir="results.tab" label="${tool.name} on ${on_string}">
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69 <filter>'TABULAR' in outputs</filter>
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70 </data>
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71 <data format="bed" name="output_region" from_work_dir="results.bed" label="${tool.name} on ${on_string} - BED file">
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72 <filter>'BED' in outputs</filter>
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73 </data>
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74 <data format="gff3" name="output_ggf_full" from_work_dir="results_full.gff" label="${tool.name} on ${on_string} - GFF file extended">
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75 <filter>'-gffFull' in outputs</filter>
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76 </data>
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77 <data format="gff3" name="output_gff" from_work_dir="results.gff" label="${tool.name} on ${on_string} - GFF file">
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78 <filter>'-gff' in outputs</filter>
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79 </data>
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80 <data format="fasta" name="output_fasta" label="${tool.name} on ${on_string} - GFF file">
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81 <filter>'-spacers' in outputs</filter>
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82 </data>
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="input" value="sequence.fasta" ftype="fasta" />
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87 <param name="minNR" value="3" />
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88 <param name="minRL" value="29" />
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89 <param name="maxRL" value="38" />
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90 <param name="minSL" value="19" />
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91 <param name="maxSL" value="48" />
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92 <param name="searchWL" value="none" />
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93 <output name="output" file="minced.tabular" ftype="tabular" />
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94 <output name="output_region" file="minced.bed" ftype="bed" />
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95 </test>
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96 </tests>
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97 <help>
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98 **What it does**
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99
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100 MinCED - Mining CRISPRs in Environmental Datasets
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101
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102
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103 MinCED is a program to find Clustered Regularly Interspaced Short Palindromic
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104 Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes,
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105 in which sequence size can be anywhere from 100 to 800 bp. MinCED runs from the
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106 command-line and was derived from CRT (http://www.room220.com/crt/).
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107
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108 https://github.com/ctSkennerton/minced
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109
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110 **Citation**
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111
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112 For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P:
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113 CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209`
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114
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115 If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools
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116
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117 </help>
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118 </tool>
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119
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