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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 3efdc8b41f4f54d034d43b833733324153771fcf
author iuc
date Mon, 02 Sep 2024 07:41:11 +0000
parents 037f0acc7830
children
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037f0acc7830 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit c142110046b4ed562e8240a65f5603640752dc2e
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1 <tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="23.0">
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2 <description>Paired-End read merger</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.9.6</token>
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5 <token name="@VERSION_SUFFIX@">4</token>
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6 <xml name="format_action">
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7 <actions>
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8 <conditional name="library.type">
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9 <when value="paired">
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10 <action type="format">
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11 <option type="from_param" name="library.forward" param_attribute="ext"/>
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12 </action>
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13 </when>
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14 <when value="paired_collection">
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15 <action type="format">
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16 <option type="from_param" name="library.input_collection" param_attribute="forward.ext"/>
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17 </action>
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18 </when>
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19 </conditional>
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20 </actions>
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21 </xml>
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22 </macros>
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23 <xrefs>
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24 <xref type="bio.tools">pear</xref>
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25 </xrefs>
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26 <requirements>
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27 <requirement type="package" version="@TOOL_VERSION@">pear</requirement>
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28 </requirements>
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29 <command detect_errors="aggressive">
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30 <![CDATA[
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31 pear
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32 #if str( $library.type ) == "paired":
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037f0acc7830 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit c142110046b4ed562e8240a65f5603640752dc2e
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33 -f '$library.forward'
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34 -r '$library.reverse'
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35 #if $library.forward.is_of_type( 'fastqillumina' ):
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36 --phred-base 64
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37 #else:
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38 --phred-base 33
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39 #end if
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40 #else
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41 ## prepare collection
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42 -f '$library.input_collection.forward'
037f0acc7830 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit c142110046b4ed562e8240a65f5603640752dc2e
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43 -r '$library.input_collection.reverse'
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44 #if $library.input_collection.forward.is_of_type( 'fastqillumina' ):
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45 --phred-base 64
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46 #else:
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47 --phred-base 33
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48 #end if
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49 #end if
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50
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51 --output pear
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52 --p-value $pvalue
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53 --min-overlap $min_overlap
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54 #if $max_assembly_length and int($max_assembly_length) > 0:
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55 --max-asm-length $max_assembly_length
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56 #end if
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57 --min-asm-length $min_assembly_length
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58 --min-trim-length $min_trim_length
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59 --quality-theshold $quality_threshold
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60 --max-uncalled-base $max_uncalled_base
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61 --test-method $test_method
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62 --threads "\${GALAXY_SLOTS:-8}"
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63 --score-method $score_method
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64 --cap $cap
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65 $empirical_freqs
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66 $nbase
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67 ]]>
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68 </command>
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69 <inputs>
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70 <conditional name="library">
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71 <param name="type" type="select" label="Dataset type">
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72 <option value="paired">Paired-end</option>
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73 <option value="paired_collection">Paired-end Dataset Collection</option>
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74 </param>
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75 <when value="paired">
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76 <param name="forward" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the forward paired-end reads" help="-f"/>
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77 <param name="reverse" type="data" format="fastqillumina,fastqsanger" label="Name of file that contains the reverse paired-end reads" help="-r"/>
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78 </when>
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79 <when value="paired_collection">
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80 <param name="input_collection" type="data_collection" format="fastqillumina,fastqsanger" label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" collection_type="paired"/>
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81 </when>
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82 </conditional>
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83 <!-- optional -->
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84 <param name="pvalue" argument="--p-value" type="float" min="0" max="1" value="0.01" label="Specify a p-value for the statistical test" help="If the computed p-value of a possible assembly exceeds the specified p-value then the paired-end read will not be assembled. Setting 1.0 disables the test. (--p-value)"/>
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85 <param argument="--min-overlap" type="integer" value="10" min="0" label="Minimum overlap size" help="The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. (--min-overlap)"/>
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86 <param argument="--max-assembly-length" min="0" type="integer" value="0" label="Maximum possible length of the assembled sequences" help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)"/>
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87 <param argument="--min-assembly-length" min="0" type="integer" value="50" label="Minimum possible length of the assembled sequences" help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short."/>
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88 <param argument="--min-trim-length" min="0" type="integer" value="1" label="Minimum length of reads after trimming the low quality part" help="See option --quality-threshold."/>
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89 <param argument="--quality-threshold" type="integer" value="0" label="Quality score threshold for trimming the low quality part of a read" help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed."/>
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90 <param argument="--max-uncalled-base" type="float" min="0" max="1" value="1.0" label="Maximal proportion of uncalled bases in a read" help="Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases."/>
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91 <param argument="--cap" type="integer" value="40" min="0" label="Specify the upper bound for the resulting quality score" help="If set to zero, capping is disabled."/>
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92 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)">
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93 <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option>
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94 <option value="2">Use the acceptance probability (2)</option>
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95 </param>
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96 <param name="empirical_freqs" type="boolean" truevalue="--empirical-freqs" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/>
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97 <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" label="Use N base if uncertain" help="When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)"/>
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98 <param name="score_method" type="select" label="Scoring method" help="(--score-method)">
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99 <option value="1">OES with +1 for match and -1 for mismatch</option>
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100 <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option>
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101 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option>
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102 </param>
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103 <param name="outputs" type="select" optional="false" label="Output files" multiple="true">
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104 <option value="assembled" selected="true">Assembled reads</option>
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105 <option value="unassembled_forward">Forward unassembled reads</option>
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106 <option value="unassembled_reverse">Reverse unassembled reads</option>
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107 <option value="discarded">Discarded reads</option>
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108 </param>
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109 </inputs>
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110 <outputs>
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111 <data name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads">
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112 <expand macro="format_action"/>
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113 <filter>'assembled' in outputs</filter>
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114 </data>
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115 <data format="auto" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads">
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116 <expand macro="format_action"/>
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117 <filter>'unassembled_forward' in outputs</filter>
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118 </data>
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119 <data format="auto" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads">
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120 <expand macro="format_action"/>
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121 <filter>'unassembled_reverse' in outputs</filter>
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122 </data>
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123 <data format="auto" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads">
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124 <expand macro="format_action"/>
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125 <filter>'discarded' in outputs</filter>
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126 </data>
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127 </outputs>
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128 <tests>
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129 <test expect_num_outputs="2">
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130 <conditional name="library">
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131 <param name="type" value="paired"/>
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132 <param name="forward" value="forward.fastq" ftype="fastqsanger"/>
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133 <param name="reverse" value="reverse.fastq" ftype="fastqsanger"/>
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134 </conditional>
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135 <param name="min_overlap" value="10"/>
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136 <param name="min_assembly_length" value="50"/>
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137 <param name="cap" value="0"/>
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138 <param name="outputs" value="assembled,unassembled_forward"/>
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139 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/>
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140 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/>
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141 </test>
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142 <!-- same test as before using collection input and fastqillumina
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143 (even if it isn't) .. therefore only loose check of outputs -->
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144 <test expect_num_outputs="2">
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145 <conditional name="library">
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146 <param name="type" value="paired_collection"/>
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147 <param name="input_collection">
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148 <collection type="paired">
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149 <element name="forward" value="forward.fastq" ftype="fastqillumina"/>
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150 <element name="reverse" value="reverse.fastq" ftype="fastqillumina"/>
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151 </collection>
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152 </param>
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153 </conditional>
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154 <param name="min_overlap" value="10"/>
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155 <param name="min_assembly_length" value="50"/>
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156 <param name="cap" value="0"/>
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157 <param name="outputs" value="assembled,unassembled_forward"/>
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158 <output name="assembled_reads" ftype="fastqillumina">
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159 <assert_contents>
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160 <has_line_matching expression="@.*"/>
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161 </assert_contents>
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162 </output>
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163 <output name="unassembled_forward_reads" ftype="fastqillumina">
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164 <assert_contents>
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165 <has_line_matching expression="@.*"/>
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166 </assert_contents>
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167 </output>
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168 </test>
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169 </tests>
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170 <help>
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171 <![CDATA[
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172
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173 **What it does**
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174
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175 PEAR_ is an ultrafast, memory-efficient and highly accurate pair-end read merger.
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176 PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment
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177 size as input. In addition, it implements a statistical test for minimizing false-positive results.
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178 Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes
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179 on a standard desktop computer.
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180
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181 For more information please look at the documentation_ and `github repository`_.
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182
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183 .. _PEAR: https://sco.h-its.org/exelixis/web/software/pear/
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184 .. _documentation: https://sco.h-its.org/exelixis/web/software/pear/doc.html
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185 .. _github repository: https://github.com/tseemann/PEAR
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186
2
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187 Please note that PEAR is released under the
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188 [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license
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189 and that commercial partners should obtain a license.
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190
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191 ]]>
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192 </help>
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193 <citations>
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194 <citation type="doi">10.1093/bioinformatics/btt593</citation>
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195 </citations>
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196 </tool>