Mercurial > repos > iuc > colibread_lordec

annotate lordec.xml @ 4:a92669266a08 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
author iuc
date Fri, 14 Aug 2020 20:54:21 +0000
parents c44f93b8ed51
children 87c61a0e1177
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a46ffa224482 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool profile="16.04" id="lordec" name="Lordec" version="0.9">
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3 <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="0.9">lordec</requirement>
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9 </requirements>
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10 <command><![CDATA[
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12 #if str( $program_type_choice.program_type ) == "correct"
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13 lordec-correct
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14 @lordec_inputs@
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15 #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced"
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16 -t ${program_type_choice.advanced_options.t}
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17 -b ${program_type_choice.advanced_options.b}
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18 -e ${program_type_choice.advanced_options.e}
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19 -T ${program_type_choice.advanced_options.T}
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20 #end if
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21 -o '${corrected_read_file}'
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24 #else if str( $program_type_choice.program_type ) == "trim"
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25 #if $program_type_choice.split
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26 lordec-trim-split
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27 #else
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28 lordec-trim
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29 #end if
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30 -i '${program_type_choice.i}'
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31 -o '${trimmed_reads_file}'
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33 #else
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34 lordec-stat
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35 @lordec_inputs@
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36 -S '${stat_file}'
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37 #end if
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38
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40 ]]></command>
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41
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42 <inputs>
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44 <conditional name="program_type_choice">
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45 <param name="program_type" type="select" label="Choose Lordec program">
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46 <option value="correct">Lordec Correct</option>
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47 <option value="trim">Lordec Trim</option>
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48 <option value="stats">Lordec Statistics</option>
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49 </param>
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50
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51 <when value="correct">
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52 <expand macro="lordec_inputs" />
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53 <conditional name="advanced_options">
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54 <param name="advanced_options_selector" type="select" label="Lordec correct advanced options">
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55 <option value="default" selected="true">Default</option>
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56 <option value="advanced">Advanced</option>
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57 </param>
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58 <when value="default"></when>
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59 <when value="advanced">
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60 <param argument="-t" type="integer" label="Number of target k-mers" value="5" />
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61 <param argument="-b" type="integer" label="Maximum number of branches to explore" value="200" />
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62 <param argument="-e" type="float" label="Maximum error rate" value="0.4" />
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63 <param argument="-T" type="integer" label="Number of threads" value="1" />
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64 </when>
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65 </conditional>
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66 </when>
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67
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68 <when value="trim">
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69 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
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70 <param name="split" type="boolean" label="Use the split option" help="Trim all weak regions and split the reads on inner weak regions" />
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71 </when>
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73 <when value="stats">
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74 <expand macro="lordec_inputs" />
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75 </when>
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76
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77 </conditional>
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79 </inputs>
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80
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81 <outputs>
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82 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
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83 <filter>program_type_choice['program_type'] == 'correct'</filter>
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84 </data>
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85 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" >
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86 <filter>program_type_choice['program_type'] == 'trim'</filter>
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87 </data>
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88 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" >
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89 <filter>program_type_choice['program_type'] == 'stats'</filter>
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90 </data>
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91 </outputs>
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92
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93 <tests>
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94 <test>
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95 <conditional name="program_type_choice">
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96 <param name="program_type" value="correct" />
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97 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
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98 <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
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99 <param name="k" value="31" />
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100 </conditional>
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101 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
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102 </test>
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103 <test>
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104 <conditional name="program_type_choice">
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105 <param name="program_type" value="trim" />
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106 <param name="i" value="lordec/corrected_reads.fa" />
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107 </conditional>
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108 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
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109 </test>
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110 <test>
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111 <conditional name="program_type_choice">
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112 <param name="program_type" value="stats" />
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113 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
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114 <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
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115 </conditional>
4
a92669266a08 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"
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116 <output name="stat_file" file="lordec/stat_file.txt" compare="sim_size" delta="10"/>
0
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117 </test>
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118 </tests>
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119 <help><![CDATA[
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120
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121 **Lordec Correct**
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122
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123 Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina).
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124
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125 LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters.
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126
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127 -------
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128
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129 **Lordec Trim**
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130
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131 Program for trimming the weak regions from the beginning and end of the corrected reads.
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132
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133 -------
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134
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135 **Lordec Statistics**
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136
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137 Program to generate statistics on solid and weak k-mers.
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138
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139 -------
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140
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141 **Web site**
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142
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143 http://www.atgc-montpellier.fr/lordec/
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144
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145
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146 ]]></help>
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147 <expand macro="citations">
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148 <citation type="doi">10.1093/bioinformatics/btu538</citation>
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149 </expand>
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150 </tool>