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1 <tool id="shrimp_wrapper" name="SHRiMP for Letter-space" version="1.0.0">
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2 <description>reads mapping against reference sequence </description>
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3 <command interpreter="python">
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4 #if ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip") #shrimp_wrapper.py $input_target $output1 $output2 $input_query
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5 #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip") #shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size
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6 #elif ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="full") #shrimp_wrapper.py $input_target $output1 $output2 $input_query $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold
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7 #elif ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="full") #shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_hit_threshold
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8 #end if#
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9 </command>
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10 <inputs>
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11 <page>
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12 <conditional name="type_of_reads">
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13 <param name="single_or_paired" type="select" label="Single- or Paired-ends">
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14 <option value="single">Single-end</option>
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15 <option value="paired">Paired-end</option>
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16 </param>
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17 <when value="single">
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18 <param name="input_query" type="data" format="fastqsolexa" label="Align sequencing reads" help="No dataset? Read tip below"/>
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19 </when>
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20 <when value="paired">
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21 <param name="insertion_size" type="integer" size="5" value="600" label="Insertion length between two ends" help="bp" />
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22 <param name="input1" type="data" format="fastqsolexa" label="Align sequencing reads, one end" />
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23 <param name="input2" type="data" format="fastqsolexa" label="and the other end" />
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24 </when>
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25 </conditional>
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26 <param name="input_target" type="data" format="fasta" label="against reference" />
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27 <conditional name="param">
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28 <param name="skip_or_full" type="select" label="SHRiMP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
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29 <option value="skip">Commonly used</option>
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30 <option value="full">Full Parameter List</option>
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31 </param>
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32 <when value="skip" />
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33 <when value="full">
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34 <param name="spaced_seed" type="text" size="30" value="111111011111" label="Spaced Seed" />
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35 <param name="seed_matches_per_window" type="integer" size="5" value="2" label="Seed Matches per Window" />
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36 <param name="seed_hit_taboo_length" type="integer" size="5" value="4" label="Seed Hit Taboo Length" />
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37 <param name="seed_generation_taboo_length" type="integer" size="5" value="0" label="Seed Generation Taboo Length" />
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38 <param name="seed_window_length" type="float" size="10" value="115.0" label="Seed Window Length" help="in percentage"/>
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39 <param name="max_hits_per_read" type="integer" size="10" value="100" label="Maximum Hits per Read" />
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40 <param name="max_read_length" type="integer" size="10" value="1000" label="Maximum Read Length" />
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41 <param name="kmer" type="integer" size="10" value="-1" label="Kmer Std. Deviation Limit" help="-1 as None"/>
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42 <param name="sw_match_value" type="integer" size="10" value="100" label="S-W Match Value" />
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43 <param name="sw_mismatch_value" type="integer" size="10" value="-150" label="S-W Mismatch Value" />
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44 <param name="sw_gap_open_ref" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Reference)" />
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45 <param name="sw_gap_open_query" type="integer" size="10" value="-400" label="S-W Gap Open Penalty (Query)" />
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46 <param name="sw_gap_ext_ref" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Reference)" />
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47 <param name="sw_gap_ext_query" type="integer" size="10" value="-70" label="S-W Gap Extend Penalty (Query)" />
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48 <param name="sw_hit_threshold" type="float" size="10" value="68.0" label="S-W Hit Threshold" help="in percentage"/>
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49 </when>
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50 </conditional>
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51 </page>
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52 </inputs>
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53 <outputs>
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54 <data name="output1" format="tabular"/>
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55 <data name="output2" format="tabular"/>
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56 </outputs>
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57 <requirements>
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58 <requirement type="binary">rmapper-ls</requirement>
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59 </requirements>
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60 <tests>
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61 <test>
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62 <param name="single_or_paired" value="single" />
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63 <param name="skip_or_full" value="skip" />
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64 <param name="input_target" value="shrimp_phix_anc.fa" ftype="fasta" />
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65 <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/>
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66 <output name="output1" file="shrimp_wrapper_test1.out1" />
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67 </test>
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68 <!--
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69 <test>
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70 <param name="single_or_paired" value="paired" />
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71 <param name="skip_or_full" value="skip" />
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72 <param name="input_target" value="shrimp_eca_chrMT.fa" ftype="fasta" />
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73 <param name="input1" value="shrimp_wrapper_test2_end1.fastq" ftype="fastqsolexa" />
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74 <param name="input2" value="shrimp_wrapper_test2_end2.fastq" ftype="fastqsolexa" />
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75 <param name="insertion_size" value="600" />
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76 <output name="output1" file="shrimp_wrapper_test2.out1" />
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77 </test>
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78 <test>
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79 <param name="single_or_paired" value="single" />
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80 <param name="skip_or_full" value="full" />
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81 <param name="input_target" value="shrimp_phix_anc.fa" ftype="fasta" />
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82 <param name="input_query" value="shrimp_wrapper_test1.fastq" ftype="fastqsolexa"/>
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83 <param name="spaced_seed" value="111111011111" />
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84 <param name="seed_matches_per_window" value="2" />
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85 <param name="seed_hit_taboo_length" value="4" />
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86 <param name="seed_generation_taboo_length" value="0" />
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87 <param name="seed_window_length" value="115.0" />
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88 <param name="max_hits_per_read" value="100" />
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89 <param name="max_read_length" value="1000" />
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90 <param name="kmer" value="-1" />
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91 <param name="sw_match_value" value="100" />
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92 <param name="sw_mismatch_value" value="-150" />
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93 <param name="sw_gap_open_ref" value="-400" />
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94 <param name="sw_gap_open_query" value="-400" />
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95 <param name="sw_gap_ext_ref" value="-70" />
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96 <param name="sw_gap_ext_query" value="-70" />
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97 <param name="sw_hit_threshold" value="68.0" />
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98 <output name="output1" file="shrimp_wrapper_test1.out1" />
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99 </test>
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100 <test>
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101 <param name="single_or_paired" value="paired" />
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102 <param name="skip_or_full" value="full" />
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103 <param name="input_target" value="shrimp_eca_chrMT.fa" ftype="fasta" />
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104 <param name="spaced_seed" value="111111011111" />
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105 <param name="seed_matches_per_window" value="2" />
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106 <param name="seed_hit_taboo_length" value="4" />
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107 <param name="seed_generation_taboo_length" value="0" />
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108 <param name="seed_window_length" value="115.0" />
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109 <param name="max_hits_per_read" value="100" />
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110 <param name="max_read_length" value="1000" />
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111 <param name="kmer" value="-1" />
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112 <param name="sw_match_value" value="100" />
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113 <param name="sw_mismatch_value" value="-150" />
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114 <param name="sw_gap_open_ref" value="-400" />
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115 <param name="sw_gap_open_query" value="-400" />
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116 <param name="sw_gap_ext_ref" value="-70" />
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117 <param name="sw_gap_ext_query" value="-70" />
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118 <param name="sw_hit_threshold" value="68.0" />
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119 <param name="input1" value="shrimp_wrapper_test2_end1.fastq" ftype="fastqsolexa"/>
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120 <param name="input2" value="shrimp_wrapper_test2_end2.fastq" ftype="fastqsolexa"/>
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121 <param name="insertion_size" value="600" />
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122 <output name="output1" file="shrimp_wrapper_test2.out1" />
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123 </test>
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124 -->
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125 </tests>
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126 <help>
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127
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128 .. class:: warningmark
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129
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130 IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64. Click pencil icon next to your dataset to set datatype to *fastqsolexa*.
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131
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132
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133 -----
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134
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135 **What it does**
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136
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137 SHRiMP (SHort Read Mapping Package) is a software package for aligning genomic reads against a target genome.
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138
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139 This wrapper post-processes the default SHRiMP/rmapper-ls output and generates a table with all information from reads and reference for the mapping. The tool takes single- or paired-end reads. For single-end reads, only uniquely mapped alignment is considered. In paired-end reads, only pairs that meet the following criteria will be used to generate the table: 1). the ends fall within the insertion size; 2). the ends are mapped at the opposite directions. If there are still multiple mappings after applying the criteria, this paired-end read will be discarded.
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140
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141
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142 -----
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143
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144 **Input formats**
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145
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146 A multiple-fastq file, for example::
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147
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148 @seq1
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149 TACCCGATTTTTTGCTTTCCACTTTATCCTACCCTT
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150 +seq1
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151 hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh
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152
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153
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154 -----
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155
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156 **Outputs**
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157
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158 The tool gives two outputs.
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159
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160 **Table output**
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161
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162 Table output contains 8 columns::
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163
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164 1 2 3 4 5 6 7 8
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165 ----------------------------------------------------
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166 chrM 14711 seq1 0 T A 40 1
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167 chrM 14712 seq1 1 T T 40 1
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168
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169 where::
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170
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171 1. (chrM) - Reference sequence id
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172 2. (14711) - Position of the mapping in the reference
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173 3. (seq1) - Read id
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174 4. (0) - Position of the mapping in the read
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175 5. (T) - Nucleotide in the reference
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176 6. (A) - Nucleotide in the read
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177 7. (40) - Quality score for the nucleotide in the position of the read
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178 8. (1) - The number of times this position is covered by reads
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179
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180
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181 **SHRiMP output**
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182
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183 This is the default output from SHRiMP/rmapper-ls::
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184
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185 1 2 3 4 5 6 7 8 9 10
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186 -------------------------------------------------------------------
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187 seq1 chrM + 3644 3679 1 36 36 3600 36
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188
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189 where::
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190
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191 1. (seq1) - Read id
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192 2. (chrM) - Reference sequence id
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193 3. (+) - Strand of the read
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194 4. (3466) - Start position of the alignment in the reference
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195 5. (3679) - End position of the alignment in the reference
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196 6. (1) - Start position of the alignment in the read
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197 7. (36) - End position of the alignment in the read
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198 8. (36) - Length of the read
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199 9. (3600) - Score
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200 10. (36) - Edit string
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201
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202
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203 -----
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204
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205 **SHRiMP parameter list**
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206
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207 The commonly used parameters with default value setting::
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208
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209 -s Spaced Seed (default: 111111011111)
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210 The spaced seed is a single contiguous string of 0's and 1's.
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211 0's represent wildcards, or positions which will always be
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212 considered as matching, whereas 1's dictate positions that
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213 must match. A string of all 1's will result in a simple kmer scan.
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214 -n Seed Matches per Window (default: 2)
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215 The number of seed matches per window dictates how many seeds
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216 must match within some window length of the genome before that
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217 region is considered for Smith-Waterman alignment. A lower
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218 value will increase sensitivity while drastically increasing
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219 running time. Higher values will have the opposite effect.
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220 -t Seed Hit Taboo Length (default: 4)
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221 The seed taboo length specifies how many target genome bases
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222 or colors must exist prior to a previous seed match in order
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223 to count another seed match as a hit.
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224 -9 Seed Generation Taboo Length (default: 0)
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225
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226 -w Seed Window Length (default: 115.00%)
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227 This parameter specifies the genomic span in bases (or colours)
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228 in which *seed_matches_per_window* must exist before the read
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229 is given consideration by the Simth-Waterman alignment machinery.
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230 -o Maximum Hits per Read (default: 100)
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231 This parameter specifies how many hits to remember for each read.
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232 If more hits are encountered, ones with lower scores are dropped
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233 to make room.
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234 -r Maximum Read Length (default: 1000)
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235 This parameter specifies the maximum length of reads that will
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236 be encountered in the dataset. If larger reads than the default
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237 are used, an appropriate value must be passed to *rmapper*.
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238 -d Kmer Std. Deviation Limit (default: -1 [None])
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239 This option permits pruning read kmers, which occur with
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240 frequencies greater than *kmer_std_dev_limit* standard
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241 deviations above the average. This can shorten running
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242 time at the cost of some sensitivity.
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243 *Note*: A negative value disables this option.
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244 -m S-W Match Value (default: 100)
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245 The value applied to matches during the Smith-Waterman score calculation.
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246 -i S-W Mismatch Value (default: -150)
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247 The value applied to mismatches during the Smith-Waterman
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248 score calculation.
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249 -g S-W Gap Open Penalty (Reference) (default: -400)
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250 The value applied to gap opens along the reference sequence
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251 during the Smith-Waterman score calculation.
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252 *Note*: Note that for backward compatibility, if -g is set
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253 and -q is not set, the gap open penalty for the query will
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254 be set to the same value as specified for the reference.
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255 -q S-W Gap Open Penalty (Query) (default: -400)
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256 The value applied to gap opens along the query sequence during
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257 the Smith-Waterman score calculation.
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258 -e S-W Gap Extend Penalty (Reference) (default: -70)
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259 The value applied to gap extends during the Smith-Waterman score calculation.
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260 *Note*: Note that for backward compatibility, if -e is set
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261 and -f is not set, the gap exten penalty for the query will
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262 be set to the same value as specified for the reference.
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263 -f S-W Gap Extend Penalty (Query) (default: -70)
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264 The value applied to gap extends during the Smith-Waterman score calculation.
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265 -h S-W Hit Threshold (default: 68.00%)
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266 In letter-space, this parameter determines the threshold
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267 score for both vectored and full Smith-Waterman alignments.
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268 Any values less than this quantity will be thrown away.
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269 *Note* This option differs slightly in meaning between letter-space and color-space.
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270
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271
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272 -----
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273
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274 **Reference**
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275
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276 **SHRiMP**: Stephen M. Rumble, Michael Brudno, Phil Lacroute, Vladimir Yanovsky, Marc Fiume, Adrian Dalca. shrimp at cs dot toronto dot edu.
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277
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278 </help>
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279 </tool>
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