Mercurial > repos > jjohnson > fgbio_trim_fastq

annotate macros.xml @ 0:604d9b0ad9a4 draft default tip

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"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
author jjohnson
date Thu, 19 Aug 2021 15:13:17 +0000
parents
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.0</token>
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3 <token name="@VERSION_SUFFIX@">1</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">fgbio</requirement>
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7 <yield/>
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8 </requirements>
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9 </xml>
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10 <xml name="citations">
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11 <citations>
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12 <citation type="bibtex">@online{fgbio,
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13 author = {Tim Fennell, Nils Homer},
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14 title = {fgbio},
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15 year = 2015,
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16 url = {https://github.com/fulcrumgenomics/fgbio},
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17 urldate = {2021-03-01}
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18 }</citation>
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19 </citations>
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20 </xml>
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21 <token name="@READ_STRUCTURE_PATTERN@">(([1-9][0-9]*[TBMS])*([+]|[1-9][0-9]*)[TBMS])</token>
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22 <token name="@READ_STRUCTURES_PATTERN@">@READ_STRUCTURE_PATTERN@(\s@READ_STRUCTURE_PATTERN@)*</token>
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23 <xml name="read_structures_validator" token_pattern="@READ_STRUCTURES_PATTERN@">
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24 <validator type="regex" message="">^@READ_STRUCTURES_PATTERN@$</validator>
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25 </xml>
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26 <xml name="read_structures" token_pattern="@READ_STRUCTURES_PATTERN@">
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27 <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
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28 <expand macro="read_structures_validator" pattern="@READ_STRUCTURE_PATTERN@" />
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29 </param>
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30 </xml>
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31
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32 <xml name="fastq_input" token_fastqtype="reads" token_defaultpaired="True" token_defaultnone="False">
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33 <conditional name="@FASTQTYPE@">
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34 <param name="type" type="select" label="Library type of FASTQ @FASTQTYPE@">
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35 <option value="none" selected="@DEFAULTNONE@">NO fastq @FASTQTYPE@</option>
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36 <option value="single">Single-end</option>
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37 <option value="paired" selected="@DEFAULTPAIRED@">Paired-end</option>
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38 <option value="paired_collection">Paired-end Dataset Collection</option>
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39 </param>
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40 <when value="none"/>
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41 <when value="single">
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42 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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43 <expand macro="read_structures" pattern="@READ_STRUCTURE_PATTERN@" />
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44 </when>
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45 <when value="paired">
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46 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads #1 in FASTQ format" />
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47 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads #2 in FASTQ format" />
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48 <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
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49 </when>
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50 <when value="paired_collection">
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51 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired Reads in FASTQ format" />
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52 <expand macro="read_structures" pattern="@READ_STRUCTURES_PATTERN@" />
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53 </when>
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54 </conditional>
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55 </xml>
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56 <xml name="fastq_reads">
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57 <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
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58 </xml>
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59 <xml name="fastq_inputs">
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60 <expand macro="fastq_input" fastqtype="reads" defaultpaired="True" defaultnone="False"/>
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61 <expand macro="fastq_input" fastqtype="indices" defaultpaired="False" defaultnone="True"/>
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62 </xml>
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63 <token name="@FASTQ_READS@"><![CDATA[
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64 #set $fastqs = []
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65 #set $read_structs = []
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66 #if $reads.type == 'single':
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67 $fastqs.append($reads.input_single)
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68 #elif $reads.type == 'paired':
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69 $fastqs.append($reads.input_read1)
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70 $fastqs.append($reads.input_read2)
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71 #elif $reads.type == 'paired_collection':
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72 $fastqs.append($reads.input_readpair.forward)
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73 $fastqs.append($reads.input_readpair.reverse)
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74 #end if
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75 #if $reads.type !='none' and $reads.read_structures:
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76 $read_structs.append(str($reads.read_structures))
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77 #end if
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78 #set $read_structures = "%s" % (' '.join($read_structs))
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79 #if $read_structs:
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80 --read-structures $read_structures
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81 #end if
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82 ]]></token>
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83 <token name="@LINK_FASTQ_INPUTS@"><![CDATA[
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84 #import re
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85 #def identifier_or_name($input1)
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86 #if hasattr($input1, 'element_identifier')
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87 #return $input1.element_identifier
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88 #else
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89 #return $input1.name
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90 #end if
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91 #end def
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92 #def clean($name1)
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93 #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fq|fastq)$','', $re.sub('.*/','', $name1.rstrip('.gz'))))
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94 #return $name_clean
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95 #end def
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96 #def ln_name($ds)
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97 #set $ext = ''
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98 #if $ds.is_of_type('mzml') or $ds.is_of_type('fastq.gz')
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99 #set $ext = ".fastq.gz"
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100 #else if $ds.is_of_type('fastq')
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101 #set $ext = ".fastq"
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102 #end if
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103 #set $name = "%s%s" % ($clean($identifier_or_name($ds)),$ext)
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104 #return $name
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105 #end def
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106 #set $fastqs = []
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107 #set $read_structs = []
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108 #if $reads.type == 'single':
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109 #set $i_name = $ln_name($reads.input_single)
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110 #silent $fastqs.append($i_name)
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111 ln -s '$reads.input_single' '$i_name' &&
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112 #elif $reads.type == 'paired':
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113 #set $f_name = $ln_name($reads.input_read1)
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parents:
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114 #silent $fastqs.append($f_name)
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parents:
diff changeset
115 ln -s '$reads.input_read1' '$f_name' &&
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jjohnson
parents:
diff changeset
116 #set $r_name = $ln_name($reads.input_read2)
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parents:
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117 #silent $fastqs.append($r_name)
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parents:
diff changeset
118 ln -s '$reads.input_read2' '$r_name' &&
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jjohnson
parents:
diff changeset
119 #elif $reads.type == 'paired_collection':
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parents:
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120 #set $f_name = $ln_name($reads.input_readpair.forward)
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parents:
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121 #silent $fastqs.append($f_name)
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parents:
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122 ln -s '$reads.input_readpair.forward' '$f_name' &&
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jjohnson
parents:
diff changeset
123 #set $r_name = $ln_name($reads.input_readpair.reverse)
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parents:
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124 #silent $fastqs.append($r_name)
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parents:
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125 ln -s '$reads.input_readpair.reverse' '$r_name' &&
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jjohnson
parents:
diff changeset
126 #end if
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127 #if $reads.type !='none' and $reads.read_structures:
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parents:
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128 $read_structs.append(str($reads.read_structures))
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jjohnson
parents:
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129 #end if
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parents:
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130 #if $indices.type == 'single':
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parents:
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131 #set $i_name = $ln_name($indices.input_single)
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parents:
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132 #silent $fastqs.append($i_name)
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parents:
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133 ln -s '$indices.input_single' '$i_name' &&
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parents:
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134 #elif $indices.type == 'paired':
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parents:
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135 #set $f_name = $ln_name($indices.input_read1)
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parents:
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136 #silent $fastqs.append($f_name)
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parents:
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137 ln -s '$indices.input_read1' '$f_name' &&
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parents:
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138 #set $r_name = $ln_name($indices.input_read2)
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parents:
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139 #silent $fastqs.append($r_name)
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parents:
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140 ln -s '$indices.input_read2' '$r_name' &&
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parents:
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141 #elif $indices.type == 'paired_collection':
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parents:
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142 #set $f_name = $ln_name($indices.input_readpair.forward)
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parents:
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143 #silent $fastqs.append($f_name)
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parents:
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144 ln -s '$indices.input_readpair.forward' '$f_name' &&
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parents:
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145 #set $r_name = $ln_name($indices.input_readpair.reverse)
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parents:
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146 #silent $fastqs.append($r_name)
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147 ln -s '$indices.input_readpair.reverse' '$r_name' &&
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148 #end if
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149 #if $indices.type != 'none' and $indices.read_structures:
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150 $read_structs.append(str($indices.read_structures))
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parents:
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151 #end if
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152 ]]></token>
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parents:
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153 <token name="@FASTQ_INPUTS@"><![CDATA[
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jjohnson
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154 --input
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155 #for $input in $fastqs
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156 '$input'
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157 #end for
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158 #set $read_structures = "%s" % (' '.join($read_structs))
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159 #if $read_structs:
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160 --read-structures $read_structures
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161 #end if
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162 ]]></token>
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163 <xml name="inherit_format_1">
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164 <actions>
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165 <conditional name="library.type">
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166 <when value="single">
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167 <action type="format">
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168 <option type="from_param" name="library.input_1" param_attribute="ext" />
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169 </action>
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170 </when>
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171 <when value="paired">
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172 <action type="format">
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173 <option type="from_param" name="library.input_1" param_attribute="ext" />
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174 </action>
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175 </when>
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176 <when value="paired_collection">
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177 <action type="format">
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178 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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179 </action>
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180 </when>
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181 </conditional>
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182 </actions>
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183 </xml>
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184
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185 <xml name="inherit_format_2">
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186 <actions>
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187 <conditional name="library.type">
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188 <when value="paired">
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189 <action type="format">
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190 <option type="from_param" name="library.input_2" param_attribute="ext" />
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191 </action>
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192 </when>
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193 <when value="paired_collection">
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194 <action type="format">
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195 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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196 </action>
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197 </when>
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198 </conditional>
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199 </actions>
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200 </xml>
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201 <xml name="sam_tag_validator">
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202
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203 <validator type="regex" message="">^[A-Za-z][A-Za-z]$</validator>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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204 </xml>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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205 <xml name="sam_sort_order">
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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parents:
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206 <param argument="--sort-order" type="select" optional="true" label="Sort BAM by">
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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207 <option value="TemplateCoordinate">TemplateCoordinate</option>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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208 <option value="Coordinate">Coordinate</option>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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parents:
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209 <option value="Queryname">Queryname</option>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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210 <option value="Random">Random</option>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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211 <option value="RandomQuery">RandomQuery</option>
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diff changeset
212 </param>
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213 </xml>
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214
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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215 <xml name="sort_order_change_format">
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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216 <change_format>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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diff changeset
217 <when input="sort_order" value="Coordinate" format="bam" />
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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diff changeset
218 <when input="sort_order" value="TemplateCoordinate" format="bam" />
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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diff changeset
219 <when input="sort_order" value="QueryName" format="unsorted.bam" />
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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diff changeset
220 <when input="sort_order" value="Random" format="unsorted.bam" />
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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diff changeset
221 <when input="sort_order" value="RandomQuery" format="unsorted.bam" />
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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diff changeset
222 </change_format>
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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223 </xml>
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224
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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diff changeset
225 <token name="@READ_STRUCTURES_HELP@"><![CDATA[
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jjohnson
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226 **Read Structures**
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227
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228 Read structures are made up of <number><operator> pairs much like the CIGAR string in BAM files. Four kinds of operators are recognized:
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229
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230 - T identifies a template read
604d9b0ad9a4 "planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
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231 - B identifies a sample barcode read
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232 - M identifies a unique molecular index read
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233 - S identifies a set of bases that should be skipped or ignored
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234
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235 The last <number><operator> pair may be specified using a + sign instead of number to denote “all remaining bases”. This is useful if, e.g., fastqs have been trimmed and contain reads of varying length. For example to convert a paired-end run with an index read and where the first 5 bases of R1 are a UMI and the second five bases are monotemplate you might specify:
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236
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237 ::
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238
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239 --input r1.fq r2.fq i1.fq --read-structures 5M5S+T +T +B
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240
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241 Alternative if you know your reads are of fixed length you could specify:
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242
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243 ::
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244
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245 --input r1.fq r2.fq i1.fq --read-structures 5M5S65T 75T 8B
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246
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247
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248 ]]></token>
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249 <xml name="citations">
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250 <citations>
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251 <yield />
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252 </citations>
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253 </xml>
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254 </macros>