Mercurial > repos > iuc > mothur_make_contigs

annotate make.contigs.xml @ 3:0f563b96b60d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:54:16 -0500
parents 4cf175b57289
children b1b4240133f5
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1 <tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.0">
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
d9268e6b2ea0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
1
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
1
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
1
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11
3
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12 ## Symlinks creation or On the fly creation of a combo file
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 #if $input_type.type == 'list_collection'
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 #for $pair in $input_type.list_paired_collection:
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s ${pair.forward} `basename ${pair.forward}` &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 ln -s ${pair.reverse} `basename ${pair.reverse}` &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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17 echo -e "${pair.name}\t`basename ${pair.forward}`\t`basename ${pair.reverse}`" >> combo_fastq.dat &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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18 #end for
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19 #elif $input_type.type == 'simple_collection'
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 ln -s '$input_type.paired_collection.forward' ffastq.dat &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 ln -s '$input_type.paired_collection.reverse' rfastq.dat &&
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22 #else
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23 ln -s '$input_type.forward_fastq' ffastq.dat &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 ln -s '$input_type.reverse_fastq' rfastq.dat &&
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25 #end if
1
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26
3
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27 #if $oligo.add == "yes":
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28 ln -s '$oligo.oligos' oligo.oligos.dat &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 ln -s '$oligo.findex' oligo.findex.dat &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 ln -s '$oligo.rindex' oligo.rindex.dat &&
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 #end if
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32
3
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33 echo 'make.contigs(
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 #if $input_type.type == 'list_collection':
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35 file=combo_fastq.dat,
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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36 #else:
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37 ffastq=ffastq.dat,
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 rfastq=rfastq.dat,
0f563b96b60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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39 #end if
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40 align=$align,
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41 #if $oligo.add == "yes":
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42 oligos=oligo.oligos.dat,
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43 bdiffs=$oligo.bdiffs,
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44 pdiffs=$oligo.pdiffs,
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45 tdiffs=$oligo.tdiffs,
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46 #if $oligo.findex:
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47 findex=oligo.findex.dat,
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48 #end if
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49 #if $oligo.rindex:
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50 rindex=oligo.rindex.dat,
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51 #end if
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52 #end if
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53 match=$match,
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54 mismatch=$mismatch,
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55 gapopen=$gapopen,
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56 gapextend=$gapextend,
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57 rename=$rename
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58 processors='\${GALAXY_SLOTS:-8}'
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59 )'
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60 | sed 's/ //g' ## mothur trips over whitespace
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61 | mothur
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62 | tee mothur.out.log
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63 ]]></command>
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64 <inputs>
1
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65 <conditional name="input_type">
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66 <param name="type" type="select" label="Select a way to provide forward and reverse fastq files ?" help="">
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67 <option value="regular" selected="true">Two simple fastq files (forward and reverse)</option>
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68 <option value="simple_collection">One pair (paired collection)</option>
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69 <option value="list_collection">Multiple pairs - Combo mode (list:paired collection)</option>
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70 </param>
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71 <when value="regular">
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72 <param name="forward_fastq" type="data" format="fastq" label="Forward reads"/>
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73 <param name="reverse_fastq" type="data" format="fastq" label="Reverse reads"/>
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74 </when>
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75 <when value="simple_collection">
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76 <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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77 </when>
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78 <when value="list_collection">
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79 <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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80 </when>
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81 </conditional>
0
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82 <param name="align" type="select" label="align - Select a pairwise alignment method" help="">
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83 <option value="needleman" selected="true">needleman (default) </option>
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84 <option value="gotoh">gotoh</option>
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85 <option value="kmer">kmer</option>
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86 </param>
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87 <conditional name="oligo">
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88 <param name="add" type="select" label="Trim with an oligos file?" help="">
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89 <option value="no">no</option>
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90 <option value="yes">yes</option>
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91 </param>
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92 <when value="no"/>
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93 <when value="yes">
1
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94 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers"
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95 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"/>
0
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96 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
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97 <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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98 <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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99 <param name="findex" type="data" format="fastq" optional="true" label="forward index file (fastq)"/>
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100 <param name="rindex" type="data" format="fastq" optional="true" label="revese index file (fastq)"/>
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101 </when>
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102 </conditional>
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103 <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
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104 <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
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105 <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
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106 <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
3
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107 <param name="rename" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Renames sequences"
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108 help="reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream.
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109 Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time"/>
0
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110 </inputs>
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111 <outputs>
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112 <expand macro="logfile-output"/>
1
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113 <data name="fasta" format="fasta" from_work_dir="*fastq.trim.*.fasta" label="${tool.name} on ${on_string}: trim.contigs.fasta"/>
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114 <data name="qual" format="qual" from_work_dir="*fastq*.trim.*.qual" label="${tool.name} on ${on_string}: trim.contigs.qual"/>
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115 <data name="scrapfasta" format="fasta" from_work_dir="*fastq*.scrap.*.fasta" label="${tool.name} on ${on_string}: scrap.contigs.fasta"/>
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116 <data name="scrapqual" format="qual" from_work_dir="*fastq*.scrap.*.qual" label="${tool.name} on ${on_string}: scrap.contigs.qual"/>
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117 <data name="report" format="txt" from_work_dir="*fastq*.contigs.report" label="${tool.name} on ${on_string}: report"/>
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118 <data name="group" format="mothur.groups" from_work_dir="*fastq*.groups" label="${tool.name} on ${on_string}: group file">
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119 <filter>input_type['type'] == 'list_collection'</filter>
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120 </data>
0
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121 </outputs>
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122 <tests>
1
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123 <!-- Test with two regular files as input -->
0
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124 <test>
1
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125 <conditional name="input_type">
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126 <param name="type" value="regular"/>
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127 <param name="forward_fastq" value="Mock_S280_L001_R1_001_small.fastq" ftype="fastq"/>
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128 <param name="reverse_fastq" value="Mock_S280_L001_R2_001_small.fastq" ftype="fastq"/>
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129 </conditional>
0
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130 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
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131 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
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132 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
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133 <expand macro="logfile-test"/>
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134 </test>
1
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135 <!-- Test with a simple paired collection as input -->
0
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136 <test>
1
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137 <conditional name="input_type">
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138 <param name="type" value="simple_collection"/>
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139 <param name="paired_collection">
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140 <collection type="paired">
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141 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
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142 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
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143 </collection>
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144 </param>
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145 </conditional>
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146 <output name="fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
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147 <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/>
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148 <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/>
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149 <expand macro="logfile-test"/>
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150 </test>
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151 <!-- Test with a simple paired collection as input + extra parameters specified -->
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152 <test>
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153 <conditional name="input_type">
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154 <param name="type" value="simple_collection"/>
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155 <param name="paired_collection">
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156 <collection type="paired">
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157 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
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158 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
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159 </collection>
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160 </param>
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161 </conditional>
0
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162 <param name="align" value="gotoh"/>
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163 <param name="match" value="2"/>
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164 <param name="mismatch" value="-2"/>
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165 <param name="gapopen" value="-3"/>
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166 <param name="gapextend" value="-2"/>
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167 <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/>
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168 <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/>
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169 <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/>
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170 <expand macro="logfile-test"/>
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171 </test>
1
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172 <!-- Test with a list:paired collection as input -->
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173 <test>
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174 <conditional name="input_type">
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175 <param name="type" value="list_collection"/>
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176 <param name="list_paired_collection">
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177 <collection type="list:paired">
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178 <element name="Pair1">
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179 <collection type="paired">
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180 <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" />
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181 <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" />
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182 </collection>
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183 </element>
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184 <element name="Pair2">
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185 <collection type="paired">
2
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186 <element name="forward" value="test_forward.fastq" />
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187 <element name="reverse" value="test_reverse.fastq" />
1
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188 </collection>
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189 </element>
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190 </collection>
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191 </param>
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192 </conditional>
2
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193 <output name="fasta" md5="91bd3b91adc6559182ad118b767f0a07" ftype="fasta"/>
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194 <output name="qual" md5="7094d1ac82a40e9f89cc6cdf5e214da7" ftype="qual"/>
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195 <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/>
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196 <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/>
1
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197 <expand macro="logfile-test"/>
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198 </test>
0
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199 </tests>
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200 <help><![CDATA[
0
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201
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202 @MOTHUR_OVERVIEW@
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203
1
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204 **Command Documentation**
0
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205
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206 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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207
1
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208 .. _make.contigs: https://www.mothur.org/wiki/Make.contigs
0
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209
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210 v.1.27.0: Updated to use Mothur 1.33. Added findex and rindex parmaeters, optionally used with the oligos file.
3
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211
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212 ]]></help>
0
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213 <expand macro="citations"/>
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214 </tool>