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annotate repenrich.xml @ 14:bf866bedd4b4 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 205141a3f695f202d5c3e01e6ab3b2b869fe62b5
author artbio
date Sat, 20 Apr 2024 12:13:52 +0000
parents 530626b0757c
children 2e3d976e7d5d
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6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
artbio
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1 <tool id="repenrich" name="RepEnrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Repeat Element Profiling</description>
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3 <macros>
6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
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4 <import>macros.xml</import>
6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
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5 </macros>
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6 <expand macro="repenrich_requirements"/>
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f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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7 <stdio>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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9 </stdio>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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10 <command detect_errors="exit_code"><![CDATA[
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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11 #import re
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d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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12 ## uncompress fastq.gz or fastqsanger.gz if needed
d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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13 #if $seq_method.seq_method_list == "single-read":
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02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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14 #if $seq_method.input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
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530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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15 gunzip < '$seq_method.input_fastq' > 'input.fastq' &&
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16 #else:
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530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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17 ln -f -s '$seq_method.input_fastq' 'input.fastq' &&
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02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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18 #end if
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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19 #elif $seq_method.seq_method_list == 'paired_collection':
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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20 #if $seq_method.input_fastq.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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21 gunzip < '$seq_method.input_fastq.forward' > 'input.fastq' &&
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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22 gunzip < '$seq_method.input_fastq.reverse' > 'input_2.fastq' &&
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02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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23 #else:
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24 ln -f -s '$seq_method.input_fastq.forward' 'input.fastq' &&
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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25 ln -f -s '$seq_method.input_fastq.reverse' 'input_2.fastq' &&
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26 #end if
d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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27 #else:
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02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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28 #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
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530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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29 gunzip < '$seq_method.input_fastq' > 'input.fastq' &&
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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30 gunzip < '$seq_method.input2_fastq' > 'input_2.fastq' &&
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d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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31 #else:
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32 ln -f -s '$seq_method.input_fastq' 'input.fastq' &&
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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33 ln -f -s '$seq_method.input2_fastq' 'input_2.fastq' &&
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34 #end if
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35 #end if
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530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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36 ln -f -s '$genome' 'genome.fa' &&
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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37 bowtie-build '$genome' genome &&
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89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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38 python $__tool_directory__/RepEnrich_setup.py
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39 --annotation_file '$repeatmasker'
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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40 --genomefasta 'genome.fa'
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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41 --cpus "\${GALAXY_SLOTS:-4}" &&
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f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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42 #if $seq_method.seq_method_list == "single-read":
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43 bowtie genome -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max multimap.fastq input.fastq input_unique.sam 2>bowtie_alignments.txt &&
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f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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44 #else:
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530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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45 bowtie genome -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max multimap.fastq -1 input.fastq -2 input_2.fastq input_unique.sam 2>bowtie_alignments.txt &&
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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46 #end if
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47 samtools view -@ \${GALAXY_SLOTS:-4} -bS 'input_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o 'input_unique.bam' &&
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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48 samtools index input_unique.bam &&
530626b0757c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit df6b9491ad06e8a85e67c663b68db3cce3eb0115
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49 python $__tool_directory__/RepEnrich.py
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50 --annotation_file $repeatmasker
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51 --alignment_bam input_unique.bam
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52 --cpus "\${GALAXY_SLOTS:-4}"
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53 #if $seq_method.seq_method_list == "single-read":
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54 --fastqfile multimap.fastq
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55 #else:
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56 --fastqfile multimap_1.fastq
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57 --fastqfile2 multimap_2.fastq
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58 #end if
0
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59 ]]></command>
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60 <!-- basic error handling -->
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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61 <inputs>
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62 <conditional name="seq_method">
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63 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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64 <option selected="True" value="single-read">Single-read sequencing</option>
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65 <option value="paired-end">Paired-end sequencing</option>
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66 <option value="paired_collection">Paired-end Dataset Collection</option>
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67 </param>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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68 <when value="single-read">
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69 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
0
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70 </when>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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71 <when value="paired-end">
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02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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72 <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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73 <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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74 </when>
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75 <when value="paired_collection">
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76 <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;" />
0
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77 </when>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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78 </conditional>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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79 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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80 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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81 </inputs>
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82
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83 <outputs>
13
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84 <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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85 <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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86 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tsv" />
0
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87 </outputs>
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88
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89 <tests>
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90 <test>
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91 <param name="seq_method_list" value="single-read"/>
13
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92 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/>
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93 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/>
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94 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/>
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95 <output name="class_fraction_counts" file="chrY_single_class_fraction_counts.tab" ftype="tabular"/>
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96 <output name="family_fraction_counts" file="chrY_single_family_fraction_counts.tab" ftype="tabular"/>
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97 <output name="fraction_counts" file="chrY_single_fraction_counts.tab" ftype="tabular"/>
0
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98 </test>
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99 <test>
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100 <param name="seq_method_list" value="paired-end"/>
13
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101 <param name="input_fastq" value="chrY-500k.R1.fastqsanger.gz" ftype="fastq.gz"/>
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102 <param name="input2_fastq" value="chrY-500k.R2.fastqsanger.gz" ftype="fastq.gz"/>
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103 <param name="genome" value="chrY-1-500k.fa" ftype="fasta"/>
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104 <param name="repeatmasker" value="chrY-1-500k.fa.out" ftype="txt"/>
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105 <output name="class_fraction_counts" file="chrY_paired_class_fraction_counts.tab" ftype="tabular"/>
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106 <output name="family_fraction_counts" file="chrY_paired_family_fraction_counts.tab" ftype="tabular"/>
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107 <output name="fraction_counts" file="chrY_paired_fraction_counts.tab" ftype="tabular"/>
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108 </test>
0
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109 </tests>
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110
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111 <help>
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112
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113 **What it does**
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114
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115 Reads are mapped to the genome using the Bowtie1 aligner. Reads mapping uniquely to the
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116 genome are assigned to subfamilies of repetitive elements based on their degree of overlap
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117 to RepeatMasker annotated genomic instances of each repetitive element subfamily.
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118
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119 Reads mapping to multiple locations are separately mapped to repetitive element assemblies
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120 – referred to as repetitive element psuedogenomes – built from RepeatMasker annotated
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121 genomic instances of repetitive element subfamilies.
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122
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123 RepEnrich then return tables of counts merged from both strategies, that can be further
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124 processed in statistical analysis for differential expression. For detailed information
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125 see the `original publication`_.
0
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126
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127 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583
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128
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129 **Inputs**
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130
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131 *Reference genome* : reference genome in fasta format
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132
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133 *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format.
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134
13
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135 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from
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136 https://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
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137
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138 This file looks like:
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139
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140 <![CDATA[
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141
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142 SW perc perc perc query position in query matching repeat position in repeat
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143
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144 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID
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145
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146 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486
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147
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148 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487
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149
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150 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488
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151
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152 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489
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153
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154 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490
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155
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156 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491
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157
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158 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492
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159
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160 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493
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162 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494
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163
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164 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495
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165
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166 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496
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168 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497
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170 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498
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172 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499
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174 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500
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176 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501
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178 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502
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179
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180 ]]>
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181
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182 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons)
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183
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184 **Outputs**
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185
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186 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned
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187 in tabular format for further statistical tests, differential expression analysis or graphics.
0
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189 **RepEnrich**
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190
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191 .. class:: warningmark
0
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192
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193 Earlier versions of the RepEnrich.py and RepEnrich_setpup.py scripts of this galaxy wrapper
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194 were directly derived from the `nskvir/RepEnrich GitHub repository`_ which is not maintained
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195 anymore.
0
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196
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197 Starting from 2024, python codes were extensively rewritten for clarity, maintenance and
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198 optimization and we now refer exclusively to our `GitHub repository`_ for code review.
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199
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200 .. _nskvir/RepEnrich GitHub repository: https://github.com/nskvir/RepEnrich
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201 .. _GitHub repository: https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich
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203 **Execution time**
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204
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205 .. class:: warningmark
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206
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207 This tool includes time-consuming steps to index the reference genome, index repeat
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208 sequences and to align reads to these indexes.
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209
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210 .. class:: infomark
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211
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212 For more information on the tools, or giving us feedback, please visit our `code repository`_.
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214 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/
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215 .. _ARTbio team: http://artbio.fr
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216
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217 </help>
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218
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219 <citations>
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220 <citation type="doi">10.1186/1471-2164-15-583</citation>
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221 </citations>
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222 </tool>