annotate repenrich2.xml @ 9:2b61c6407efb draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit 961a14cd73dd8e40b2f30d5e4df136b98cd8f07a
author artbio
date Thu, 25 Apr 2024 16:22:34 +0000
parents 388a47ca4199
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1 <tool id="repenrich2" name="RepEnrich2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Repeat Element Profiling</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 <expand macro="repenrich_requirements"/>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12 ## uncompress fastq.gz or fastqsanger.gz is not required with bowtie2
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13 #if $seq_method.seq_method_list == "single-read":
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14 ln -f -s '$seq_method.input_fastq' 'input.fastq' &&
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15 #elif $seq_method.seq_method_list == 'paired_collection':
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16 ln -f -s '$seq_method.input_fastq.forward' 'input.fastq' &&
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17 ln -f -s '$seq_method.input_fastq.reverse' 'input_2.fastq' &&
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18 #else:
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19 ln -f -s '$seq_method.input_fastq' 'input.fastq' &&
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20 ln -f -s '$seq_method.input2_fastq' 'input_2.fastq' &&
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21 #end if
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22
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23 #if $refGenomeSource.genomeSource == "history":
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24 bowtie2-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource.genome genome 1>/dev/null &&
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25 ln -s -f '$refGenomeSource.genome' 'genome.fa' &&
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26 #set index_path = 'genome'
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27 #else:
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28 #set index_path = $refGenomeSource.genome.fields.path
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29 ln -s '${index_path}.fa' 'genome.fa' &&
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30 #end if
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31
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32 python $__tool_directory__/RepEnrich2_setup.py
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33 --annotation_file '$repeatmasker'
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34 --genomefasta 'genome.fa'
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35 --cpus "\${GALAXY_SLOTS:-4}" &&
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36
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37 #if $seq_method.seq_method_list == "single-read":
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38 bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} input.fastq
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39 | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 &&
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40 samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b -q 38 aligned.bam -o unique.bam &&
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41 samtools view -@ "\${GALAXY_SLOTS:-4}" -F 4 -b aligned.bam
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42 | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null &&
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43 bedtools bamtofastq -i filt_aligned.bam -fq multimap.fastq &&
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44 #else:
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45 bowtie2 -x $index_path -p \${GALAXY_SLOTS:-4} -1 input.fastq -2 input_2.fastq
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46 | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o aligned.bam 2>&1 &&
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47 samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b -q 38 aligned.bam -o unique.bam &&
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48 samtools view -@ "\${GALAXY_SLOTS:-4}" -f 3 -b aligned.bam
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49 | samtools view -@ "\${GALAXY_SLOTS:-4}" -U filt_aligned.bam -bq 38 - > /dev/null &&
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50 samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -n filt_aligned.bam
0
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51 | bedtools bamtofastq -i /dev/stdin -fq multimap_1.fastq -fq2 multimap_2.fastq &&
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52 #end if
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53 samtools index unique.bam &&
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54
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55
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56 python $__tool_directory__/RepEnrich2.py
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57 --annotation_file $repeatmasker
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58 --alignment_bam unique.bam
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59 --cpus "\${GALAXY_SLOTS:-4}"
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60 #if $seq_method.seq_method_list == "single-read":
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61 --fastqfile multimap.fastq
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62 #else:
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63 --fastqfile multimap_1.fastq
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64 --fastqfile2 multimap_2.fastq
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65 #end if
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66 ]]></command>
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67 <!-- basic error handling -->
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68 <inputs>
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69 <conditional name="seq_method">
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70 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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71 <option selected="True" value="single-read">Single-read sequencing</option>
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72 <option value="paired-end">Paired-end sequencing</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="single-read">
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76 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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77 </when>
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78 <when value="paired-end">
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79 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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80 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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81 </when>
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82 <when value="paired_collection">
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83 <param name="input_fastq" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
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84 </when>
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85 </conditional>
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86 <conditional name="refGenomeSource">
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87 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
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88 <option value="indexed">Use a built-in index</option>
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89 <option value="history">Use one from the history</option>
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90 </param>
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91 <when value="indexed">
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92 <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="genome" type="select">
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93 <options from_data_table="bowtie2_indexes" />
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94 </param>
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95 </when>
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96 <when value="history">
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97 <param format="fasta" label="Select a fasta file, to serve as index reference" name="genome" type="data" />
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98 </when>
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99 </conditional>
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100
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101 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
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102 </inputs>
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103
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104 <outputs>
5
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105 <data format="tabular" name="unique_mapper_counts" label="RepEnrich on ${on_string}: unique mapper counts" from_work_dir="unique_mapper_counts.tsv" />
0
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106 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tsv" />
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107 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tsv" />
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108 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tsv" />
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109 </outputs>
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110
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111 <tests>
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112 <test>
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113 <param name="seq_method_list" value="single-read"/>
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114 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/>
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115 <param name="genomeSource" value="history"/>
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116 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/>
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117 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/>
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118 <output name="unique_mapper_counts" file="chrY_single_unique_mapper_counts.tab" ftype="tabular"/>
0
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119 <output name="class_fraction_counts" file="chrY_single_class_fraction_counts.tab" ftype="tabular"/>
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120 <output name="family_fraction_counts" file="chrY_single_family_fraction_counts.tab" ftype="tabular"/>
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121 <output name="fraction_counts" file="chrY_single_fraction_counts.tab" ftype="tabular"/>
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122 </test>
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123 <test>
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124 <param name="seq_method_list" value="paired-end"/>
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125 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/>
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126 <param name="input2_fastq" value="chrY-500k.R2.fastqsanger.gz" ftype="fastq.gz"/>
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127 <param name="genomeSource" value="history"/>
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128 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/>
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129 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/>
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130 <output name="unique_mapper_counts" file="chrY_paired_unique_mapper_counts.tab" ftype="tabular"/>
0
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131 <output name="class_fraction_counts" file="chrY_paired_class_fraction_counts.tab" ftype="tabular"/>
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132 <output name="family_fraction_counts" file="chrY_paired_family_fraction_counts.tab" ftype="tabular"/>
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133 <output name="fraction_counts" file="chrY_paired_fraction_counts.tab" ftype="tabular"/>
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134 </test>
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135 </tests>
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136
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137 <help>
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138
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139 **What it does**
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140
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141 Reads are mapped to the genome using the Bowtie2 aligner. Reads mapping uniquely to the
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142 genome are assigned to subfamilies of repetitive elements based on their degree of overlap
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143 to RepeatMasker annotated genomic instances of each repetitive element subfamily.
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144
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145 Reads mapping to multiple locations are separately mapped to repetitive element assemblies
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146 – referred to as repetitive element psuedogenomes – built from RepeatMasker annotated
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147 genomic instances of repetitive element subfamilies.
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148
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149 RepEnrich then return tables of counts merged from both strategies, that can be further
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150 processed in statistical analysis for differential expression. For information on the method,
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151 see the `original publication`_.
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152
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153 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583
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154
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155 **Inputs**
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156
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157 *Reference genome* : reference genome in fasta format
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158
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159 *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format.
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160
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161 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from
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162 https://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
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163
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164 This file looks like:
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165
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166 <![CDATA[
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167
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168 SW perc perc perc query position in query matching repeat position in repeat
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169
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170 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID
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171
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172 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486
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173
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174 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487
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175
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176 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488
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177
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178 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489
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180 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490
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182 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491
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184 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492
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186 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493
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188 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494
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190 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495
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192 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496
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194 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497
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196 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498
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198 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499
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200 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500
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202 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501
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204 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502
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206 ]]>
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208 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons)
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210 **Outputs**
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212 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned
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213 in tabular format for further statistical tests, differential expression analysis or graphics.
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215 **RepEnrich2**
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217 .. class:: warningmark
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219 the repenrich2 Galaxy wrapper was derived from the repenrich Galaxy wrapper
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221 repenrich2 uses bowtie2 for all alignment operations. We refer exclusively to our
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222 `GitHub repository`_ for code review.
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223
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224 .. _GitHub repository: https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2
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226 **Execution time**
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228 .. class:: warningmark
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229
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230 This tool includes time-consuming steps to index the reference genome, index repeat
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231 sequences and to align reads to these indexes.
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233 </help>
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235 <citations>
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236 <citation type="doi">10.1186/1471-2164-15-583</citation>
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237 </citations>
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238 </tool>