annotate hisat2_macros.xml @ 11:e926afbd9e10 draft

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author iuc
date Mon, 10 Apr 2017 23:17:56 -0400
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children f4fa77189eb0
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="function" tokens="helptext">
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4 <param display="radio" help="@HELPTEXT@" label="Function type" name="function_type" type="select">
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5 <option value="C">Constant</option>
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6 <option value="L">Linear [f(x) = y + z * x]</option>
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7 <option value="S">Square root [f(x) = y + z * x&#178;]</option>
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8 <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option>
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9 </param>
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10 <param help="@HELPTEXT@" label="Constant term (y)" name="constant_term" type="integer" value="0" />
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11 <param help="@HELPTEXT@" label="Coefficient (z)" name="coefficient" type="integer" value="0" />
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12 </xml>
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13 <xml name="single_paired_selector">
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14 <param label="Single end or paired reads?" name="paired_selector" type="select">
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15 <option value="paired_collection">Collection of paired reads</option>
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16 <option value="paired">Individual paired reads</option>
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17 <option value="single">Individual unpaired reads</option>
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18 </param>
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19 </xml>
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20 <xml name="paired_input_conditional" tokens="ftype">
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21 <conditional name="paired">
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22 <expand macro="single_paired_selector" />
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23 <when value="paired_collection">
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24 <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
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25 <expand macro="paired_end_conditional" />
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26 <expand macro="paired_end_output" />
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27 </when>
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28 <when value="paired">
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29 <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" />
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30 <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" />
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31 <expand macro="paired_end_conditional" />
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32 <expand macro="paired_end_output" />
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33 </when>
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34 <when value="single">
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35 <param format="@FTYPE@" label="Reads" name="reads" type="data" />
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36 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un / --un-gz" />
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37 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al / --al-gz" />
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38 </when>
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39 </conditional>
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40 </xml>
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41 <xml name="paired_end_conditional">
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42 <conditional name="paired_end_options">
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43 <param label="Paired-end options" name="paired_end_options_selector" type="select">
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44 <option value="defaults">Use default values</option>
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45 <option value="advanced">Specify paired-end parameters</option>
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46 </param>
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47 <when value="defaults" />
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48 <when value="advanced">
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49 <param name="no_mixed" label="Disable alignments of individual mates" type="boolean" truevalue="--no-mixed" falsevalue=""
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50 help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior. (--no-mixed)" />
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51 <param name="no_discordant" label="Disable discordant alignments" type="boolean" truevalue="--no-discordant" falsevalue=""
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52 help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior. (--no-discordant)" />
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53 <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) If --norc is specified, hisat will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." />
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54 </when>
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55 </conditional>
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56 </xml>
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57 <xml name="paired_end_output">
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58 <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un-conc / --un-conc-gz" />
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59 <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al-conc / --al-conc-gz" />
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60 </xml>
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61 <token name="@paired_end_options@">
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62 #if str( $input_format.paired.unaligned_file ) == "true":
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63 #if $compressed == "GZ":
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64 --un-conc-gz '${output_unaligned_reads_l}'
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65 #else if $compressed == "BZ2":
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66 --un-conc-bz2 '${output_unaligned_reads_l}'
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67 #else:
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68 --un-conc '${output_unaligned_reads_l}'
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69 #end if
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70 #end if
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71 #if str( $input_format.paired.aligned_file ) == "true":
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72 #if $compressed == "GZ":
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73 --al-conc-gz '${output_aligned_reads_l}'
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74 #else if $compressed == "BZ2"
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75 --al-conc-bz2 '${output_aligned_reads_l}'
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76 #else:
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77 --al-conc '${output_aligned_reads_l}'
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78 #end if
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79 #end if
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80 #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
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81 ${input_format.paired.paired_end_options.no_mixed}
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82 ${input_format.paired.paired_end_options.no_discordant}
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83 #end if
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84 </token>
2
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85 <token name="@strandedness_parameters@">
0
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86 #if str($spliced_options.spliced_options_selector) == "advanced":
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87 #if str($spliced_options.rna_strandness).strip() != '':
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88 --rna-strandness $spliced_options.rna_strandness
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89 #end if
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90 #end if
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91 </token>
10
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92 <token name="@FASTQGZ_SETUP@">
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93 <![CDATA[
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94 #set compressed="False"
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95 #if str($input_format.paired.paired_selector) == 'paired':
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96 #if $input_format.paired.reads_f.is_of_type("fastq.gz", "fastqsanger.gz"):
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97 #set read1 = "input_f.fastq.gz"
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98 #set compressed = "GZ"
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99 #else if $input_format.paired.reads_f.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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100 #set read1 = "input_f.fastq.bz2"
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101 #set compressed = "BZ2"
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102 #else:
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103 #set read1 = "input_f.fastq"
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104 #end if
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105 ln -f -s '${input_format.paired.reads_f}' ${read1} &&
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106
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107 #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"):
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108 #set read2 = "input_r.fastq.gz"
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109 #set compressed = "GZ"
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110 #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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111 #set read2 = "input_r.fastq.bz2"
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112 #set compressed = "BZ2"
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113 #else:
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114 #set read2 = "input_r.fastq"
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115 #end if
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116 ln -f -s '${input_format.paired.reads_r}' ${read2} &&
10
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117 #else if str($input_format.paired.paired_selector) == 'paired_collection':
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118 #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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119 #set read1 = "input_f.fastq.gz"
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120 #set compressed = "GZ"
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121 #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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122 #set read1 = "input_f.fastq.bz2"
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123 #set compressed = "BZ2"
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124 #else:
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125 #set read1 = "input_f.fastq"
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126 #end if
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127 ln -s '${input_format.paired.reads.forward}' ${read1} &&
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128
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129 #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
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130 #set read2 = "input_r.fastq.gz"
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131 #set compressed = "GZ"
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132 #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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133 #set read2 = "input_r.fastq.bz2"
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134 #set compressed = "BZ2"
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135 #else:
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136 #set read2 = "input_r.fastq"
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137 #end if
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138 ln -s '${input_format.paired.reads.reverse}' ${read2} &&
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139 #else:
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140 #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):
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141 #set read1 = "input_f.fastq.gz"
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142 #set compressed = "GZ"
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143 #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"):
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144 #set read1 = "input_f.fastq.bz2"
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145 #set compressed = "BZ2"
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146 #else:
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147 #set read1 = "input_f.fastq"
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148 #end if
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149 ln -s '${input_format.paired.reads}' ${read1} &&
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150 #end if
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151 ]]>
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152 </token>
0
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153 </macros>