Mercurial > repos > iuc > mothur_make_contigs

annotate make.contigs.xml @ 11:7238968f58f7 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 12:08:44 +0000
parents 829bb93d3add
children
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829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
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1 <tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.1">
0
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2 <description>Aligns paired forward and reverse fastq files to contigs as 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>
11
7238968f58f7 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@
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12
2
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13 ## Symlinks creation or On the fly creation of a combo file
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14 #if $input_type.type == 'list_collection'
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15 #for $pair in $input_type.list_paired_collection:
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16 ln -s ${pair.forward} `basename ${pair.forward}` &&
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17 ln -s ${pair.reverse} `basename ${pair.reverse}` &&
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18 echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
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19 #end for
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20 #elif $input_type.type == 'simple_collection'
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21 ln -s '$input_type.paired_collection.forward' ffastq.dat &&
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22 ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
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23 #else
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24 ln -s '$input_type.forward_fastq' ffastq.dat &&
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25 ln -s '$input_type.reverse_fastq' rfastq.dat &&
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26 #end if
0
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27
2
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28 #if $oligo.add == "yes":
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29 ln -s '$oligo.oligos' oligo.oligos.dat &&
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30 ln -s '$oligo.findex' oligo.findex.dat &&
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31 ln -s '$oligo.rindex' oligo.rindex.dat &&
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32 #end if
0
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33
2
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34 echo 'make.contigs(
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35 #if $input_type.type == 'list_collection':
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36 file=combo_fastq.dat,
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37 #else:
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38 ffastq=ffastq.dat,
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39 rfastq=rfastq.dat,
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40 #end if
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41 align=$align,
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42 #if $oligo.add == "yes":
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43 oligos=oligo.oligos.dat,
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44 bdiffs=$oligo.bdiffs,
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45 pdiffs=$oligo.pdiffs,
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46 tdiffs=$oligo.tdiffs,
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47 #if $oligo.findex:
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48 findex=oligo.findex.dat,
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49 #end if
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50 #if $oligo.rindex:
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51 rindex=oligo.rindex.dat,
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52 #end if
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53 #end if
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54 match=$match,
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55 mismatch=$mismatch,
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56 gapopen=$gapopen,
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57 gapextend=$gapextend,
8
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58 rename=$rename,
2
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59 processors='\${GALAXY_SLOTS:-8}'
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60 )'
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61 | sed 's/ //g' ## mothur trips over whitespace
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62 | mothur
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63 | tee mothur.out.log
0
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64 ]]></command>
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65 <inputs>
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66 <conditional name="input_type">
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67 <param name="type" type="select" label="Select a way to provide forward and reverse fastq files ?" help="">
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68 <option value="regular" selected="true">Two simple fastq files (forward and reverse)</option>
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69 <option value="simple_collection">One pair (paired collection)</option>
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70 <option value="list_collection">Multiple pairs - Combo mode (list:paired collection)</option>
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71 </param>
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72 <when value="regular">
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73 <param name="forward_fastq" type="data" format="fastq" label="Forward reads"/>
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74 <param name="reverse_fastq" type="data" format="fastq" label="Reverse reads"/>
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75 </when>
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76 <when value="simple_collection">
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77 <param name="paired_collection" type="data_collection" format="fastq" collection_type="paired" label="Fastq pair (collection)" help="Dataset collection made from a single pair of fastq files (forward + reverse)"/>
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78 </when>
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79 <when value="list_collection">
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80 <param name="list_paired_collection" type="data_collection" format="fastq" collection_type="list:paired" label="Fastq pairs (collection)" help="Dataset collection made from multiple pairs of fastq files" />
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81 </when>
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82 </conditional>
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83 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
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84 <option value="needleman" selected="true">needleman (default) </option>
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85 <option value="gotoh">gotoh</option>
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86 <option value="kmer">kmer</option>
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87 </param>
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88 <conditional name="oligo">
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89 <param name="add" type="select" label="Trim with an oligos file?" help="">
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90 <option value="no">no</option>
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91 <option value="yes">yes</option>
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92 </param>
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93 <when value="no"/>
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94 <when value="yes">
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95 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers"
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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96 help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot; and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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97 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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98 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
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99 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
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100 <param name="findex" type="data" format="fastq" optional="true" label="forward index file (fastq)"/>
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101 <param name="rindex" type="data" format="fastq" optional="true" label="revese index file (fastq)"/>
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102 </when>
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103 </conditional>
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104 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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105 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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106 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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107 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
2
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108 <param name="rename" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Renames sequences"
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109 help="reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream.
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110 Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time"/>
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111 <expand macro="param-savelog"/>
0
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112 </inputs>
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113 <outputs>
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114 <expand macro="logfile-output"/>
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115 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
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116 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
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117 <data name="scrapfasta" format="fasta" from_work_dir="*fastq*.scrap.*.fasta" label="${tool.name} on ${on_string}: scrap.contigs.fasta"/>
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118 <data name="scrapqual" format="qual" from_work_dir="*fastq*.scrap.*.qual" label="${tool.name} on ${on_string}: scrap.contigs.qual"/>
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119 <data name="report" format="txt" from_work_dir="*fastq*.contigs.report" label="${tool.name} on ${on_string}: report"/>
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120 <data name="group" format="mothur.groups" from_work_dir="*fastq*.groups" label="${tool.name} on ${on_string}: group file">
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121 <filter>input_type['type'] == 'list_collection'</filter>
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122 </data>
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123 </outputs>
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124 <tests>
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125 <!-- Test with two regular files as input -->
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126 <test>
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127 <conditional name="input_type">
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128 <param name="type" value="regular"/>
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129 <param name="forward_fastq" value="Mock_S280_L001_R1_001_small.fastq" ftype="fastq"/>
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130 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/>
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131 </conditional>
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132 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
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133 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
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134 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
2
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135 <param name="savelog" value="true"/>
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136 <param name="rename" value="false"/>
0
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137 <expand macro="logfile-test"/>
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138 </test>
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139 <!-- Test with a simple paired collection as input -->
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140 <test>
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141 <conditional name="input_type">
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142 <param name="type" value="simple_collection"/>
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143 <param name="paired_collection">
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144 <collection type="paired">
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145 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
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146 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
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147 </collection>
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148 </param>
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149 </conditional>
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150 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
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151 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
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152 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
2
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153 <param name="savelog" value="true"/>
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154 <param name="rename" value="false"/>
0
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155 <expand macro="logfile-test"/>
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156 </test>
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157 <!-- Test with a simple paired collection as input + extra parameters specified -->
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158 <test>
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159 <conditional name="input_type">
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160 <param name="type" value="simple_collection"/>
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161 <param name="paired_collection">
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162 <collection type="paired">
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163 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
164 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
165 </collection>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
166 </param>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
167 </conditional>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
168 <param name="align" value="gotoh"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
169 <param name="match" value="2"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
170 <param name="mismatch" value="-2"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
171 <param name="gapopen" value="-3"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
172 <param name="gapextend" value="-2"/>
8
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
173 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
174 <assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
175 <has_text text=">M00967_43_000000000-A3JHG_1_1101_19936_3208" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
176 </assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
177 </output>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
178 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
179 <assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
180 <has_text text=">M00967_43_000000000-A3JHG_1_1101_19936_3208" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
181 </assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
182 </output>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
183 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
184 <assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
185 <has_line line="M00967_43_000000000-A3JHG_1_1101_19936_3208&#009;253&#009;249&#009;2&#009;251&#009;0&#009;0" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
186 </assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
187 </output>
2
bfe5103b1e8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 1
diff changeset
188 <param name="savelog" value="true"/>
8
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
189 <param name="rename" value="false"/>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
190 <expand macro="logfile-test"/>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
191 </test>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
192 <!-- Test with a simple paired collection as input + rename sequences -->
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
193 <test>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
194 <conditional name="input_type">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
195 <param name="type" value="simple_collection"/>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
196 <param name="paired_collection">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
197 <collection type="paired">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
198 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
199 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
200 </collection>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
201 </param>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
202 </conditional>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
203 <output name="fasta" md5="addcc2f4233df75ab9e5feacadb6850f" ftype="fasta">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
204 <assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
205 <has_text text=">1" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
206 </assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
207 </output>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
208 <output name="qual" md5="476932c0236a672c0c99cada2b114fe7" ftype="qual">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
209 <assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
210 <has_text text=">1" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
211 </assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
212 </output>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
213 <output name="report" md5="7634bcab8db8907f80087da03259012a" ftype="txt">
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
214 <assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
215 <has_line line="1&#009;253&#009;249&#009;2&#009;251&#009;0&#009;0" />
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
216 </assert_contents>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
217 </output>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
218 <param name="savelog" value="true"/>
829bb93d3add "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd"
iuc
parents: 2
diff changeset
219 <param name="rename" value="true"/>
0
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
220 <expand macro="logfile-test"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
221 </test>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
222 <!-- Test with a list:paired collection as input -->
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
223 <test>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
224 <conditional name="input_type">
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
225 <param name="type" value="list_collection"/>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
226 <param name="list_paired_collection">
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
227 <collection type="list:paired">
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
228 <element name="Pair1">
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
229 <collection type="paired">
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
230 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
231 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
232 </collection>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
233 </element>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
234 <element name="Pair2">
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
235 <collection type="paired">
1
3dab7d200c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
iuc
parents: 0
diff changeset
236 <element name="forward" value="test_forward.fastq" />
3dab7d200c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
iuc
parents: 0
diff changeset
237 <element name="reverse" value="test_reverse.fastq" />
0
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
238 </collection>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
239 </element>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
240 </collection>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
241 </param>
2b3fac454f43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
242 </conditional>
1
3dab7d200c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
iuc
parents: 0
diff changeset
243 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/>
3dab7d200c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
iuc
parents: 0
diff changeset
244 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/>
3dab7d200c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
iuc
parents: 0
diff changeset
245 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
3dab7d200c10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
iuc
parents: 0
diff changeset
246 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
2
bfe5103b1e8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 1
diff changeset
247 <param name="savelog" value="true"/>
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248 <param name="rename" value="false"/>
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249 <expand macro="logfile-test"/>
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250 </test>
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251 </tests>
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252 <help><![CDATA[
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253
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254 @MOTHUR_OVERVIEW@
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255
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256 **Command Documentation**
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257
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258 The make.contigs_ command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.
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259
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260 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs
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261
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262 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
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263
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264 ]]></help>
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265 <expand macro="citations"/>
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266 </tool>