Mercurial > repos > iuc > pear

annotate pear.xml @ 3:b4c6f054210a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
author iuc
date Mon, 04 Apr 2022 08:31:45 +0000
parents 2f804526f5fd
children 037f0acc7830
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3
b4c6f054210a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
iuc
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1 <tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="20.09">
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2 <description>Paired-End read merger</description>
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b4c6f054210a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
iuc
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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@">2</token>
b4c6f054210a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
iuc
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6 <xml name="format_action">
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7 <actions>
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iuc
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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" />
b4c6f054210a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
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12 </action>
b4c6f054210a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
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13 </when>
b4c6f054210a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
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14 <when value="paired_collection">
b4c6f054210a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
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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 <stdio>
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30 <exit_code range="1:" />
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31 <exit_code range=":-1" />
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32 <regex match="Error:" />
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33 <regex match="Exception:" />
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34 </stdio>
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35 <command>
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36 <![CDATA[
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37 pear
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38 #if str( $library.type ) == "paired":
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39 -f "$library.forward"
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40 -r "$library.reverse"
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41 #if $library.forward.is_of_type( 'fastqillumina' ):
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42 --phred-base 64
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43 #else:
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44 --phred-base 33
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45 #end if
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46 #else
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47 ## prepare collection
1
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48 -f "$library.input_collection.forward"
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49 -r "$library.input_collection.reverse"
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50 #if $library.input_collection.forward.is_of_type( 'fastqillumina' ):
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51 --phred-base 64
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52 #else:
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53 --phred-base 33
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54 #end if
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55 #end if
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56
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57 --output pear
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58 --p-value $pvalue
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59 --min-overlap $min_overlap
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60 #if int($max_assembly_length) > 0:
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61 --max-asm-length $max_assembly_length
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62 #end if
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63 --min-asm-length $min_assembly_length
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64 --min-trim-length $min_trim_length
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65 --quality-theshold $quality_threshold
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66 --max-uncalled-base $max_uncalled_base
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67 --test-method $test_method
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68 --empirical-freqs $empirical_freqs
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69 -j "\${GALAXY_SLOTS:-8}"
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70 --score-method $score_method
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71 --cap $cap
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72 $nbase
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73 ]]>
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74 </command>
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75 <inputs>
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76 <conditional name="library">
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77 <param name="type" type="select" label="Dataset type">
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78 <option value="paired">Paired-end</option>
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79 <option value="paired_collection">Paired-end Dataset Collection</option>
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80 </param>
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81 <when value="paired">
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82 <param name="forward" type="data" format="fastqillumina,fastqsanger"
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83 label="Name of file that contains the forward paired-end reads" help="-f" />
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84 <param name="reverse" type="data" format="fastqillumina,fastqsanger"
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85 label="Name of file that contains the reverse paired-end reads" help="-r" />
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86 </when>
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87 <when value="paired_collection">
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88 <param name="input_collection" format="fastqillumina,fastqsanger"
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89 type="data_collection" collection_type="paired"
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90 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" />
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91 </when>
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92 </conditional>
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93
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94 <!-- optional -->
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95 <param name="pvalue" type="float" value="0.01" min="0" optional="true" max="1" label="Specify a p-value for the statistical test"
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96 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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97
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98 <param name="min_overlap" type="integer" value="10" optional="true" label="Minimum overlap size"
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99 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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100
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101 <param name="max_assembly_length" type="integer" value="0" optional="true" label="Maximum possible length of the assembled sequences"
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102 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. (--max-assembly-length)" />
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103
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104 <param name="min_assembly_length" type="integer" value="50" optional="true" label="Minimum possible length of the assembled sequences"
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105 help="Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. (--min-assembly-length)" />
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106
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107 <param name="min_trim_length" type="integer" value="1" optional="true" label="Minimum length of reads after trimming the low quality part"
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108 help="See option -q. (--min-trim-length)" />
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109
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110 <param name="quality_threshold" type="integer" value="0" optional="true" label="Quality score threshold for trimming the low quality part of a read"
0
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111 help="If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. (--quality-threshold)" />
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112
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113 <param name="max_uncalled_base" type="float" value="1.0" min="0" optional="true" max="1" label="Maximal proportion of uncalled bases in a read"
0
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114 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. (--max-uncalled-base)" />
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115
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116 <param name="cap" type="integer" value="40" optional="true" label="Specify the upper bound for the resulting quality score"
0
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117 help="If set to zero, capping is disabled. (--cap)" />
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118
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119 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)">
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120 <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option>
0
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121 <option value="2">Use the acceptance probability (2)</option>
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122 </param>
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123
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124 <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false"
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125 label="Disable empirical base frequencies" help="(--empirical-freqs)" />
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126 <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false"
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127 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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128
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129 <param name="score_method" type="select" label="Scoring method" help="(--score-method)">
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130 <option value="1">OES with +1 for match and -1 for mismatch</option>
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131 <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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132 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option>
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133 </param>
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134
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135 <param name="outputs" type="select" optional="false" multiple="true" label="Output files">
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136 <option value="assembled" selected="true">Assembled reads</option>
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137 <option value="unassembled_forward">Forward unassembled reads</option>
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138 <option value="unassembled_reverse">Reverse unassembled reads</option>
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139 <option value="discarded">Discarded reads</option>
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140 </param>
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141 </inputs>
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142 <outputs>
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143 <data name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads">
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144 <expand macro="format_action"/>
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145 <filter>'assembled' in outputs</filter>
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146 </data>
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147 <data format="auto" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads">
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148 <expand macro="format_action"/>
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149 <filter>'unassembled_forward' in outputs</filter>
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150 </data>
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151 <data format="auto" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads">
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152 <expand macro="format_action"/>
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153 <filter>'unassembled_reverse' in outputs</filter>
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154 </data>
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155 <data format="auto" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads">
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156 <expand macro="format_action"/>
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157 <filter>'discarded' in outputs</filter>
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158 </data>
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159 </outputs>
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160 <tests>
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161 <test expect_num_outputs="2">
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162 <conditional name="library">
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163 <param name="type" value="paired"/>
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164 <param name="forward" value="forward.fastq" ftype="fastqsanger" />
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165 <param name="reverse" value="reverse.fastq" ftype="fastqsanger" />
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166 </conditional>
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167 <param name="min_overlap" value="10" />
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168 <param name="min_assembly_length" value="50" />
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169 <param name="cap" value="0" />
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170 <param name="outputs" value="assembled,unassembled_forward" />
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171 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/>
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172 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/>
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173 </test>
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174 <!-- same test as before using collection input and fastqillumina
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175 (even if it isn't) .. therefore only loose check of outputs -->
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176 <test expect_num_outputs="2">
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177 <conditional name="library">
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178 <param name="type" value="paired_collection"/>
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179 <param name="input_collection">
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180 <collection type="paired">
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181 <element name="forward" value="forward.fastq" ftype="fastqillumina" />
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182 <element name="reverse" value="reverse.fastq" ftype="fastqillumina" />
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183 </collection>
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184 </param>
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185 </conditional>
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186 <param name="min_overlap" value="10" />
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187 <param name="min_assembly_length" value="50" />
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188 <param name="cap" value="0" />
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189 <param name="outputs" value="assembled,unassembled_forward" />
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190 <output name="assembled_reads" ftype="fastqillumina">
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191 <assert_contents>
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192 <has_line_matching expression="@.*"/>
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193 </assert_contents>
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194 </output>
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195 <output name="unassembled_forward_reads" ftype="fastqillumina">
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196 <assert_contents>
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197 <has_line_matching expression="@.*"/>
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198 </assert_contents>
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199 </output>
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200 </test>
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201 </tests>
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202 <help>
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203 <![CDATA[
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204
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205 **What it does**
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206
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207 PEAR_ is an ultrafast, memory-efficient and highly accurate pair-end read merger.
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208 PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment
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209 size as input. In addition, it implements a statistical test for minimizing false-positive results.
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210 Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes
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211 on a standard desktop computer.
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212
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213 For more information please look at the documentation_ and `github repository`_.
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214
2
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215 .. _PEAR: https://sco.h-its.org/exelixis/web/software/pear/
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216 .. _documentation: https://sco.h-its.org/exelixis/web/software/pear/doc.html
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217 .. _github repository: https://github.com/tseemann/PEAR
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218
2
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219 Please note that PEAR is released under the
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220 [CC Attribution-NonCommercial-ShareAlike](https://creativecommons.org/licenses/by-nc-sa/3.0/) license
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221 and that commercial partners should obtain a license.
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222
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223 ]]>
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224 </help>
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225 <citations>
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226 <citation type="doi">10.1093/bioinformatics/btt593</citation>
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227 </citations>
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228 </tool>