annotate pal_finder_wrapper.xml @ 2:b6ccc7dd7b02 draft

Version 0.02.04.3.
author pjbriggs
date Fri, 04 Dec 2015 07:43:30 -0500
parents 771ebe02636f
children e1a14ed7a9d6
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1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.3">
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2 <description>Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them</description>
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3 <requirements>
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4 <requirement type="package" version="5.16.3">perl</requirement>
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5 <requirement type="package" version="0.02.04">pal_finder</requirement>
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6 <requirement type="package" version="2.0.0">primer3_core</requirement>
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7 <requirement type="package" version="1.65">biopython</requirement>
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8 <requirement type="package" version="2.8.1">pandaseq</requirement>
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9 </requirements>
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10 <command interpreter="bash">pal_finder_wrapper.sh
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11 #if str( $platform.platform_type ) == "illumina"
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12 #set $paired_input_type = $platform.paired_input_type_conditional.paired_input_type
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13 #if $paired_input_type == "pair_of_files"
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14 "$platform.paired_input_type_conditional.input_fastq_r1"
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15 "$platform.paired_input_type_conditional.input_fastq_r2"
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16 #else
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17 "$platform.paired_input_type_conditional.input_fastq_pair.forward"
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18 "$platform.paired_input_type_conditional.input_fastq_pair.reverse"
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19 #end if
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20 #else
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21 --454 "$platform.input_fasta"
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22 #end if
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23 $output_microsat_summary $output_pal_summary
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24 #if $keep_config_file
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25 --output_config_file "$output_config_file"
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26 #end if
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27 --primer-prefix "$primer_prefix"
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28 --2merMinReps $min_2mer_repeats
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29 --3merMinReps $min_3mer_repeats
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30 --4merMinReps $min_4mer_repeats
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31 --5merMinReps $min_5mer_repeats
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32 --6merMinReps $min_6mer_repeats
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33 #if str( $primer.primer_options ) == "custom"
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34 --primer-opt-size $primer.primer_opt_size
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35 --primer-min-size $primer.primer_min_size
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36 --primer-max-size $primer.primer_max_size
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37 --primer-min-gc $primer.primer_min_gc
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38 --primer-max-gc $primer.primer_max_gc
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39 --primer-gc-clamp $primer.primer_gc_clamp
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40 --primer-max-end-gc $primer.primer_max_end_gc
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41 --primer-min-tm $primer.primer_min_tm
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42 --primer-max-tm $primer.primer_max_tm
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43 --primer-opt-tm $primer.primer_opt_tm
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44 --primer-pair-max-diff-tm $primer.primer_pair_max_diff_tm
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45 #end if
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46 #if str( $mispriming.mispriming_options ) == "custom"
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47 --primer-mispriming-library $mispriming.mispriming_library
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48 #end if
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49 #if str( $platform.platform_type ) == "illumina"
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50 #if $platform.filters
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51 #for $filter in str($platform.filters).split(',')
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52 $filter
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53 --filter_microsats "$output_filtered_microsats"
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54 #end for
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55 #end if
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56 #if str( $platform.assembly ) == '-assembly'
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57 $platform.assembly "$output_assembly"
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58 #end if
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59 #end if
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60 </command>
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61 <inputs>
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62 <param name="primer_prefix" type="text" value="test" size="25" label="Primer prefix" help="This prefix will be added to the beginning of all primer names" />
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63 <conditional name="platform">
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64 <param name="platform_type" type="select" label="Sequencing platform used to generate data" help="Currently pal_finder only handles Illumina paired-end reads and 454 single-end reads" >
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65 <option value="illumina" selected="true">Illumina</option>
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66 <option value="454">454</option>
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67 </param>
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68 <when value="illumina">
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69 <conditional name="paired_input_type_conditional">
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70 <param name="paired_input_type" type="select" label="Input Type">
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71 <option value="pair_of_files" selected="true">Pair of datasets</option>
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72 <option value="collection">Dataset collection pair</option>
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73 </param>
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74 <when value="pair_of_files">
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75 <param name="input_fastq_r1" type="data" format="fastqsanger"
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76 label="Illumina fastq file (read 1)" />
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77 <param name="input_fastq_r2" type="data" format="fastqsanger"
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78 label="Illumina fastq file (read 2)" />
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79 </when>
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80 <when value="collection">
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81 <param name="input_fastq_pair" format="fastqsanger"
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82 type="data_collection" collection_type="paired"
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83 label="Select FASTQ dataset collection with R1/R2 pair" />
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84 </when>
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85 </conditional>
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86 <param name="filters" type="select" display="checkboxes"
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87 multiple="True" label="Filters to apply to the pal_finder results"
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88 help="Apply none, one or more filters to refine results">
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89 <option value="-primers" selected="True">Only include loci with designed primers</option>
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90 <option value="-occurrences" selected="True">Exclude loci where the primer sequences occur more than once in the reads</option>
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91 <option value="-rankmotifs" selected="True">Only include loci with 'perfect' motifs, and rank by motif size</option>
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92 </param>
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93 <param name="assembly" type="boolean"
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94 checked="True" truevalue="-assembly" falsevalue=""
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95 label="Use PANDAseq to assemble paired-end reads and confirm primer sequences are present in high-quality assembly" />
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96 </when>
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97 <when value="454">
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98 <param name="input_fasta" type="data" format="fasta" label="454 fasta file with raw reads" />
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99 </when>
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100 </conditional>
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101 <param name="min_2mer_repeats" type="integer" value="6" label="Minimum number of 2-mer repeat units to detect" help="Set to zero to ignore repeats of this n-mer unit" />
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102 <param name="min_3mer_repeats" type="integer" value="0" label="Minimum number of 3-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" />
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103 <param name="min_4mer_repeats" type="integer" value="0" label="Minimum number of 4-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" />
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104 <param name="min_5mer_repeats" type="integer" value="0" label="Minimum number of 5-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" />
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105 <param name="min_6mer_repeats" type="integer" value="0" label="Minimum number of 6-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" />
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106 <conditional name="mispriming">
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107 <param name="mispriming_options" type="select" label="Mispriming library to use" help="Specify file of nucleotide sequences to avoid amplifying (PRIMER_MISPRIMING_LIBRARY)">
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108 <option value="default">Default from pal_finder</option>
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109 <option value="custom">Custom sequences from history</option>
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110 </param>
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111 <when value="default">
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112 </when>
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113 <when value="custom">
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114 <param name="mispriming_library" type="data" format="fasta" label="Select mispriming library from history" help="Fasta file containing sequences to avoid amplifying" />
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115 </when>
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116 </conditional>
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117 <conditional name="primer">
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118 <param name="primer_options" type="select" label="Primer settings to use" help="Advanced users can customise the settings for primer3 for more control">
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119 <option value="default">Defaults for pal_finder</option>
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120 <option value="custom">Custom</option>
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121 </param>
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122 <when value="custom">
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123 <param name="primer_opt_size" type="integer" value="20"
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124 label="Optimum length (in bases) of a primer (PRIMER_OPT_SIZE)"
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125 help="Primer3 will attempt to pick primers close to this length" />
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126 <param name="primer_min_size" type="integer" value="18"
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127 label="Minimum acceptable length (in bases) of a primer (PRIMER_MIN_SIZE)"
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128 help="Must be greater than 0 and less than or equal to PRIMER_MAX_SIZE" />
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129 <param name="primer_max_size" type="integer" value="30"
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130 label="Maximum acceptable length (in bases) of a primer (PRIMER_MAX_SIZE)"
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131 help="Currently this parameter cannot be larger than 35. This limit is governed by maximum oligo size for which primer3's melting-temperature is valid" />
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132 <param name="primer_min_gc" type="float" value="30.0"
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133 label="Minimum allowable percentage of Gs and Cs in any primer (PRIMER_MIN_GC)" />
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134 <param name="primer_max_gc" type="float" value="80.0"
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135 label="Maximum allowable percentage of Gs and Cs in any primer (PRIMER_MAX_GC)" />
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136 <param name="primer_gc_clamp" type="integer" value="2"
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137 label="Specify number of consecutive Gs and Cs at 3' end of both the left and right primer (PRIMER_GC_CLAMP)" />
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138 <param name="primer_max_end_gc" type="integer" value="5"
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139 label="Maximum number of Gs or Cs allowed in last five 3' bases of a left or right primer (PRIMER_MAX_END_GC)" />
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140 <param name="primer_min_tm" type="float" value="58.0"
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141 label="Minimum acceptable melting temperature for a primer oligo (PRIMER_MIN_TM)"
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142 help="Temperature should be in degrees Celsius" />
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143 <param name="primer_max_tm" type="float" value="65.0"
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144 label="Maximum acceptable melting temperature for a primer oligo (PRIMER_MAX_TM)"
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145 help="Temperature should be in degrees Celsius" />
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146 <param name="primer_opt_tm" type="float" value="62.0"
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147 label="Optimum melting temperature for a primer (PRIMER_OPT_TM)"
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148 help="Temperature should be in degrees Celsius" />
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pjbriggs
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149 <param name="primer_pair_max_diff_tm" type="float" value="2.0"
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150 label="Maximum acceptable difference between melting temperatures of left and right primers (PRIMER_PAIR_MAX_DIFF_TM)"
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151 help="Temperature should be in degrees Celsius" />
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pjbriggs
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152 </when>
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153 </conditional>
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pjbriggs
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154 <param name="keep_config_file" type="boolean" truevalue="True" falsevalue="False"
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pjbriggs
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155 label="Output the config file to the history"
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pjbriggs
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156 help="Can be used to run pal_finder outside of Galaxy" />
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157 </inputs>
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158 <outputs>
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159 <data name="output_pal_summary" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: all microsatellites (full details)" />
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160 <data name="output_filtered_microsats" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: filtered microsatellites (full details)">
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161 <filter>platform['platform_type'] == 'illumina' and platform['filters'] is not None</filter>
0
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162 </data>
2
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163 <data name="output_microsat_summary" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: summary of microsatellite types" />
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164 <data name="output_assembly" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: assembly">
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165 <filter>platform['assembly'] is True</filter>
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166 </data>
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167 <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: config file">
0
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168 <filter>keep_config_file is True</filter>
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169 </data>
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170 </outputs>
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171 <tests>
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172 <test>
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173 <!-- Test with Illumina input -->
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174 <param name="platform_type" value="illumina" />
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175 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
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176 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
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177 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
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178 <output name="output_pal_summary" file="illuminaPE_microsats.out" />
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179 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" />
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180 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
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181 </test>
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182 <test>
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183 <!-- Test with Illumina input as dataset pair -->
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184 <param name="platform_type" value="illumina" />
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185 <param name="paired_input_type" value="collection" />
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186 <param name="input_fastq_pair">
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187 <collection type="paired">
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188 <element name="forward" value="illuminaPE_r1.fq" ftype="fastqsanger" />
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189 <element name="reverse" value="illuminaPE_r2.fq" ftype="fastqsanger" />
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190 </collection>
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191 </param>
0
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192 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
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193 <output name="output_pal_summary" file="illuminaPE_microsats.out" />
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194 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" />
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195 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
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196 </test>
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197 <test>
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198 <!-- Test with Illumina input filter to loci with PandaSEQ assembly
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199 ('-assembly' option) -->
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200 <param name="platform_type" value="illumina" />
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201 <param name="filters" value="" />
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202 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
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203 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
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204 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
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205 <output name="output_pal_summary" file="illuminaPE_microsats.out" />
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206 <output name="output_assembly" file="illuminaPE_assembly.out" />
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207 </test>
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208 <test>
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209 <!-- Test with Illumina input filter to loci with primers
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210 ('-primers' option) -->
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211 <param name="platform_type" value="illumina" />
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212 <param name="filters" value="-primers" />
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213 <param name="assembly" value="false" />
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214 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
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215 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
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pjbriggs
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216 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
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217 <output name="output_pal_summary" file="illuminaPE_microsats.out" />
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218 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_primers.out" />
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219 </test>
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220 <test>
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221 <!-- Test with Illumina input filter to loci which appear only once
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222 ('-occurrences' option) -->
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223 <param name="platform_type" value="illumina" />
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224 <param name="filters" value="-occurrences" />
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225 <param name="assembly" value="false" />
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226 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
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227 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
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pjbriggs
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228 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
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229 <output name="output_pal_summary" file="illuminaPE_microsats.out" />
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230 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_occurrences.out" />
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231 </test>
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232 <test>
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233 <!-- Test with Illumina input filter and rank loci with perfect motifs
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234 ('-rankmotifs' option) -->
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pjbriggs
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235 <param name="platform_type" value="illumina" />
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pjbriggs
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236 <param name="filters" value="-rankmotifs" />
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pjbriggs
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237 <param name="assembly" value="false" />
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238 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
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239 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
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240 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" />
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241 <output name="output_pal_summary" file="illuminaPE_microsats.out" />
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242 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_rankmotifs.out" />
0
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243 </test>
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244 <test>
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pjbriggs
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245 <!-- Test with 454 input -->
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pjbriggs
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246 <param name="platform_type" value="454" />
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pjbriggs
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247 <param name="input_fasta" value="454_in.fa" ftype="fasta" />
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pjbriggs
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248 <output name="output_microsat_summary" file="454_microsat_types.out" />
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pjbriggs
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249 <output name="output_pal_summary" file="454_microsats.out" />
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pjbriggs
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250 </test>
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251 </tests>
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pjbriggs
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252 <help>
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pjbriggs
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253 .. class:: infomark
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pjbriggs
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254
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pjbriggs
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255 **What it does**
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256
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257 This tool runs the pal_finder program, which finds microsatellite repeat elements
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258 directly from raw 454 or Illumina paired-end sequencing reads. It then designs PCR
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pjbriggs
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259 primers to amplify these repeat loci (Potentially Amplifiable Loci: PAL).
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260
2
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261 Optionally for Illumina data, one or more filters can be applied to the output from
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262 pal_finder to:
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263
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264 * Only include loci with designed primers
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265 * Exclude loci where the primer sequences occur more than once in the reads
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266 * Only include loci with 'perfect' motifs (and rank by motif size,largest to
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267 smallest)
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268 * Use PANDAseq to assemble paired-end reads and confirm primer sequences are
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269 present in high-quality assembly
0
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270
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271 Pal_finder runs the primer3_core program; information on the settings used in
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272 primer3_core can be found in the Primer3 manual at
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273 http://primer3.sourceforge.net/primer3_manual.htm
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274
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pjbriggs
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275 -------------
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276
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277 .. class:: infomark
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278
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pjbriggs
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279 **Credits**
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280
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281 This Galaxy tool has been developed by Peter Briggs within the Bioinformatics Core
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282 Facility at the University of Manchester. It runs the pal_finder package which can be
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pjbriggs
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283 obtained from http://sourceforge.net/projects/palfinder/:
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284
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285 * PLoS One. 2012; 7(2): e30953 "Rapid Microsatellite Identification from Illumina Paired-End
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286 Genomic Sequencing in Two Birds and a Snake" Todd A. Castoe, Alexander W. Poole, A. P.
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287 Jason de Koning, Kenneth L. Jones, Diana F. Tomback, Sara J. Oyler-McCance, Jennifer A.
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288 Fike, Stacey L. Lance, Jeffrey W. Streicher, Eric N. Smith, and David D. Pollock
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289
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290 The paper is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279355/
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291
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292 This tool is compatible with pal_finder version 0.02.04, which in turn runs the
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293 primer3_core program (version 2.0.0-alpha is required, available from
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pjbriggs
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294 http://primer3.sourceforge.net/releases.php):
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295
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296 * Steve Rozen and Helen J. Skaletsky (2000) "Primer3 on the WWW for general users and for
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297 biologist programmers". In: Krawetz S, Misener S (eds) Bioinformatics Methods and
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pjbriggs
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298 Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386
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299
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300 The paper is available at
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301 http://purl.com/STEVEROZEN/papers/rozen-and-skaletsky-2000-primer3.pdf
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302
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303 The filtering and assembly of the pal_finder output for Illumina data is performed
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304 using a Python utility written by Graeme Fox at the University of Manchester, and which
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305 is included with this tool; this utility uses the BioPython and PANDAseq packages.
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306
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307 Please kindly acknowledge both this Galaxy tool, the pal_finder and primer3 packages, and
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308 the utility script and its dependencies if you use it in your work.
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309 </help>
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310 <citations>
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311 <!--
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312 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
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313 Can be either DOI or Bibtex
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314 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
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315 -->
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316 <citation type="doi">10.1371/journal.pone.0030953</citation>
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317 <citation type="bibtex">@Article{pmid10547847,
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318 Author="Rozen, S. and Skaletsky, H. ",
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319 Title="{{P}rimer3 on the {W}{W}{W} for general users and for biologist programmers}",
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320 Journal="Methods Mol. Biol.",
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321 Year="2000",
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322 Volume="132",
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323 Pages="365--386",
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324 URL="{http://purl.com/STEVEROZEN/papers/rozen-and-skaletsky-2000-primer3.pdf}"
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325 }</citation>
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326 <citation type="doi">10.1093/bioinformatics/btp163</citation>
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327 <citation type="doi">10.1186/1471-2105-13-31</citation>
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328 </citations>
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329 </tool>