Mercurial > repos > iuc > mothur_fastq_info

annotate fastq.info.xml @ 10:22da6f6c5be8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:19:04 +0000
parents 1aa945e00ef2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_fastq_info" name="Fastq.info" version="@WRAPPER_VERSION@.0">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Convert fastq to fasta and quality</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
10
22da6f6c5be8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
0
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12
2
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13 ## create symlinks to input datasets
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$fastq' fastq.dat &&
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 #if $oligo.add == "yes":
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16 ln -s '$oligo.oligos' oligo.oligos.dat &&
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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17 #end if
0
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18
2
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19 echo 'fastq.info(
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 fastq=fastq.dat,
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21 pacbio=$pacbio,
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22 format=$format
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23 #if $oligo.add == "yes":
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 ,oligos=oligo.oligos.dat
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 ,bdiffs=$oligo.bdiffs
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26 ,pdiffs=$oligo.pdiffs
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27 ,tdiffs=$oligo.tdiffs
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28 ,ldiffs=$oligo.ldiffs
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29 ,sdiffs=$oligo.sdiffs
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30 #end if
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31 )'
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32 | sed 's/ //g' ## mothur trips over whitespace
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 | mothur
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34 | tee mothur.out.log
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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35 ## rename some outputs
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36 #if $oligo.add == "yes":
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37 && mv fastq.scrap.fasta scrap.fasta
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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38 && mv fastq.scrap.qual scrap.qual
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39 #end if
0
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40 ]]></command>
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41 <inputs>
2
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42 <param argument="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/>
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43 <param argument="pacbio" type="boolean" truevalue="true" falsevalue="false" checked="false"
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44 label="pacbio - if set to true, quality scores of 0 will results in a corresponding base of N"/>
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45 <param argument="format" type="select" label="format of sequence">
0
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46 <option value="sanger" selected="true">sanger</option>
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47 <option value="solexa">solexa</option>
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48 <option value="illumina">illumina</option>
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49 <option value="illumina1.8+">illumina1.8+</option>
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50 </param>
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51 <conditional name="oligo">
2
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52 <param name="add" type="select" label="Use oligos file?"
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53 help="a file that contain the sequences of the forward and reverse primers and barcodes and their sample identifier.
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54 Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot;
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55 or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file.">
0
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56 <option value="no">no</option>
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57 <option value="yes">yes</option>
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58 </param>
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59 <when value="yes">
2
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60 <param argument="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
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61 <param argument="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/>
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62 <param argument="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/>
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63 <param argument="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0)"/>
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64 <param argument="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/>
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65 <param argument="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/>
0
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66 </when>
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67 <when value="no"/>
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68 </conditional>
2
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69 <expand macro="param-savelog"/>
0
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70 </inputs>
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71 <outputs>
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72 <expand macro="logfile-output"/>
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73 <data name="fasta_out" format="fasta" from_work_dir="fastq*.fasta" label="${tool.name} on ${on_string}: fasta"/>
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74 <data name="qfile_out" format="qual454" from_work_dir="fastq*.qual" label="${tool.name} on ${on_string}: qual"/>
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75 <data name="fastq_scrap_out" format="fastq" from_work_dir="fastq*.scrap.fastq" label="${tool.name} on ${on_string}: fastq scrap">
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76 <filter>oligos</filter>
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77 </data>
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78 <data name="fasta_scrap_out" format="fasta" from_work_dir="scrap.fasta" label="${tool.name} on ${on_string}: fasta scrap">
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79 <filter>oligos</filter>
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80 </data>
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81 <data name="qfile_scrap_out" format="qual454" from_work_dir="scrap.qual" label="${tool.name} on ${on_string}: qual scrap">
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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82 <filter>oligos</filter>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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83 </data>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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84 </outputs>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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85 <tests>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 <test>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 <param name="pacbio" value="false"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 <param name="format" value="sanger"/>
2
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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90 <param name="oligo|add" value="no"/>
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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91 <output name="fasta_out" ftype="fasta">
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92 <assert_contents>
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93 <expand macro="test-fasta-format"/>
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94 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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95 </assert_contents>
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96 </output>
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97 <output name="qfile_out">
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98 <assert_contents>
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99 <expand macro="test-qfile-format"/>
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100 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
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101 </assert_contents>
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102 </output>
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103 <param name="savelog" value="true"/>
0
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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104 <expand macro="logfile-test"/>
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105 </test>
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106 <test>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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107 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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108 <param name="pacbio" value="false"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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109 <param name="format" value="sanger"/>
2
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110 <param name="oligo|add" value="yes"/>
0
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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111 <param name="oligos" value="GQY1XT001.oligos"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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112 <param name="bdiffs" value="1"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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113 <param name="pdiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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114 <param name="tdiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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115 <param name="ldiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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116 <param name="sdiffs" value="7"/>
2
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117 <output name="fasta_out" ftype="fasta">
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118 <assert_contents>
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119 <expand macro="test-fasta-format"/>
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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120 </assert_contents>
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121 </output>
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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122 <output name="qfile_out" ftype="qual454">
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123 <assert_contents>
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124 <expand macro="test-qfile-format"/>
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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125 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
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126 </assert_contents>
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127 </output>
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128 <output name="fastq_scrap_out" ftype="fastq">
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129 <assert_contents>
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130 <expand macro="test-fastq-format"/>
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131 <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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132 </assert_contents>
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133 </output>
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134 <output name="fasta_scrap_out" ftype="fasta">
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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135 <assert_contents>
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136 <expand macro="test-fasta-format"/>
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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137 </assert_contents>
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138 </output>
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139 <output name="qfile_scrap_out" ftype="qual454">
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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140 <assert_contents>
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141 <expand macro="test-qfile-format"/>
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142 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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143 </assert_contents>
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144 </output>
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145 <param name="savelog" value="true"/>
0
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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146 <expand macro="logfile-test"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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147 </test>
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148 <test>
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149 <param name="fastq" value="Mock_S280_L001_R1_001_small.fastq"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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150 <param name="pacbio" value="false"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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151 <param name="format" value="sanger"/>
2
1aa945e00ef2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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152 <param name="oligo|add" value="yes"/>
0
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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153 <param name="oligos" value="HMPv5-v3_1368-1369.oligos"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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154 <param name="bdiffs" value="1"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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155 <param name="pdiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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156 <param name="tdiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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157 <param name="ldiffs" value="3"/>
19316e7c4802 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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158 <param name="sdiffs" value="7"/>
2
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159 <output name="fasta_out">
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160 <assert_contents>
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161 <expand macro="test-fasta-format"/>
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162 </assert_contents>
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163 </output>
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164 <output name="qfile_out">
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165 <assert_contents>
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166 <expand macro="test-qfile-format"/>
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167 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
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168 </assert_contents>
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169 </output>
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170 <output name="fastq_scrap_out">
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171 <assert_contents>
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172 <expand macro="test-fastq-format"/>
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173 <has_text text="@M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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174 </assert_contents>
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175 </output>
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176 <output name="fasta_scrap_out">
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177 <assert_contents>
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178 <expand macro="test-fasta-format"/>
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179 </assert_contents>
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180 </output>
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181 <output name="qfile_scrap_out">
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182 <assert_contents>
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183 <expand macro="test-qfile-format"/>
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184 <has_text text="M00967_43_000000000-A3JHG_1_1101_4525_7317"/>
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185 </assert_contents>
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186 </output>
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187 <param name="savelog" value="true"/>
0
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188 <expand macro="logfile-test"/>
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189 </test>
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190 </tests>
2
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191 <help><![CDATA[
0
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192
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193 @MOTHUR_OVERVIEW@
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194
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195 **Command Documentation**
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196
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197 The fastq.info_ command reads a fastq file and creates a fasta and quality file.
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198
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199
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200 .. _fastq.info: https://www.mothur.org/wiki/Fastq.info
2
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201
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202 ]]></help>
0
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203 <expand macro="citations"/>
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204 </tool>