Mercurial > repos > iuc > colibread_lordec

annotate lordec.xml @ 6:434af4cbf682 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
author iuc
date Thu, 06 May 2021 12:39:45 +0000
parents 87c61a0e1177
children 552041078feb
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6
434af4cbf682 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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1 <tool id="lordec" name="Lordec" version="0.9+galaxy2" profile="@PROFILE@">
0
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2 <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
2
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7 <requirement type="package" version="0.9">lordec</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
434af4cbf682 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 8d37fef93da141323cc120b5fec737432e497dcf"
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10 #if str( $program_type_choice.program_type ) == "correct":
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11 lordec-correct
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12 @lordec_inputs@
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13 #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced":
0
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14 -t ${program_type_choice.advanced_options.t}
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15 -b ${program_type_choice.advanced_options.b}
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16 -e ${program_type_choice.advanced_options.e}
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17 #end if
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18 -T \${GALAXY_SLOTS:-1}
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19 -o '${corrected_read_file}'
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20 #else if str( $program_type_choice.program_type ) == "trim":
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21 #if $program_type_choice.split
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22 lordec-trim-split
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23 #else
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24 lordec-trim
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25 #end if
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26 -i '${program_type_choice.i}'
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27 -o '${trimmed_reads_file}'
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28 #else
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29 lordec-stat
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30 @lordec_inputs@
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31 -S '${stat_file}'
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32 #end if
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33 ]]></command>
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34 <inputs>
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35 <conditional name="program_type_choice">
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36 <param name="program_type" type="select" label="Choose Lordec program">
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37 <option value="correct">Lordec Correct</option>
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38 <option value="trim">Lordec Trim</option>
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39 <option value="stats">Lordec Statistics</option>
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40 </param>
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41 <when value="correct">
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42 <expand macro="lordec_inputs" />
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43 <conditional name="advanced_options">
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44 <param name="advanced_options_selector" type="select" label="Lordec correct advanced options">
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45 <option value="default" selected="true">Default</option>
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46 <option value="advanced">Advanced</option>
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47 </param>
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48 <when value="default"></when>
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49 <when value="advanced">
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50 <param argument="-t" type="integer" label="Number of target k-mers" value="5" />
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51 <param argument="-b" type="integer" label="Maximum number of branches to explore" value="200" />
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52 <param argument="-e" type="float" label="Maximum error rate" value="0.4" />
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53 </when>
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54 </conditional>
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55 </when>
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56 <when value="trim">
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57 <param argument="-i" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Long read FASTA/Q file" help="PacBio reads files" />
0
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58 <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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59 </when>
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60 <when value="stats">
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61 <expand macro="lordec_inputs" />
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62 </when>
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63 </conditional>
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64 </inputs>
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65 <outputs>
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66 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
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67 <filter>program_type_choice['program_type'] == 'correct'</filter>
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68 </data>
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69 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" >
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70 <filter>program_type_choice['program_type'] == 'trim'</filter>
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71 </data>
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72 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" >
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73 <filter>program_type_choice['program_type'] == 'stats'</filter>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <test>
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78 <conditional name="program_type_choice">
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79 <param name="program_type" value="correct" />
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80 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" ftype="fasta.gz"/>
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81 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
0
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82 <param name="k" value="31" />
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83 </conditional>
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84 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
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85 </test>
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86 <test>
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87 <conditional name="program_type_choice">
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88 <param name="program_type" value="trim" />
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89 <param name="i" value="lordec/corrected_reads.fa" ftype="fasta"/>
0
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90 </conditional>
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91 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
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92 </test>
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93 <test>
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94 <conditional name="program_type_choice">
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95 <param name="program_type" value="stats" />
6
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96 <param name="inputs" value="lordec/ill-test-5K-1.fa.gz,lordec/ill-test-5K-2.fa.gz" />
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97 <param name="i" value="lordec/coli-pacbio-test-mini.fa.gz" />
0
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98 </conditional>
4
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99 <output name="stat_file" file="lordec/stat_file.txt" compare="sim_size" delta="10"/>
0
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100 </test>
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101 </tests>
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102 <help><![CDATA[
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103
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104 **Lordec Correct**
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105
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106 Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina).
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107
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108 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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109
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110 -------
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111
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112 **Lordec Trim**
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113
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114 Program for trimming the weak regions from the beginning and end of the corrected reads.
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115
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116 -------
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117
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118 **Lordec Statistics**
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119
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120 Program to generate statistics on solid and weak k-mers.
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121
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122 -------
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123
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124 **Web site**
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125
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126 http://www.atgc-montpellier.fr/lordec/
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127
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128
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129 ]]></help>
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130 <expand macro="citations">
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131 <citation type="doi">10.1093/bioinformatics/btu538</citation>
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132 </expand>
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133 </tool>