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annotate repenrich.xml @ 12:89e05f831259 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
author artbio
date Mon, 18 Mar 2024 09:39:44 +0000
parents 6bba3e33c2e7
children 530626b0757c
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11
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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artbio
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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>
6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
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6 <expand macro="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
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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12 #set input_base = 'Sample'
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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13 #set baseReference = 'Genome'
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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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d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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15 ## 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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16 #if $seq_method.seq_method_list == "single-read":
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17 #if $seq_method.input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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18 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
4
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19 #else:
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20 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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21 #end if
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22 #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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23 #if $seq_method.input_fastq.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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24 gunzip < '$seq_method.input_fastq.forward' > '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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25 gunzip < '$seq_method.input_fastq.reverse' > '${input_base}_2.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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26 #else:
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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27 ln -f -s '$seq_method.input_fastq.forward' '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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28 ln -f -s '$seq_method.input_fastq.reverse' '${input_base}_2.fastq' &&
4
d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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29 #end if
d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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30 #else:
5
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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31 #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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32 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
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33 gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' &&
4
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34 #else:
5
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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35 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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36 ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' &&
4
d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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37 #end if
d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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38 #end if
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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39 ln -f -s '$genome' '${baseReference}.fa' &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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40 bowtie-build '$genome' ${baseReference} &&
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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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41 python $__tool_directory__/RepEnrich_setup.py
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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42 --annotation_file $repeatmasker
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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43 --genomefasta ${baseReference}.fa
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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44 --setup_folder setup_folder_${baseReference} &&
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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45 #if $seq_method.seq_method_list == "single-read":
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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46 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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47 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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48 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
2
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49 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
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50 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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51 #else:
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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52 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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53 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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54 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
2
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55 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
15e3e29f310e planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
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56 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
0
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57 #end if
11
6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
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58 samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' &&
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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59 samtools index ${input_base}_unique.bam &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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60 #if $seq_method.seq_method_list == "single-read":
12
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61 python $__tool_directory__/RepEnrich.py
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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62 --annotation_file $repeatmasker
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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63 --outputfolder ${input_base}
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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64 --outputprefix ${input_base}
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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65 --setup_folder setup_folder_${baseReference}
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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66 --fastqfile ${input_base}_multimap.fastq
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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67 --alignment_bam ${input_base}_unique.bam
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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68 --cpus "\${GALAXY_SLOTS:-4}" &&
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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69 #else:
12
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
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70 python $__tool_directory__/RepEnrich.py
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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71 --annotation_file $repeatmasker
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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72 --outputfolder ${input_base}
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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73 --outputprefix ${input_base}
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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74 --setup_folder setup_folder_${baseReference}
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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75 --fastqfile ${input_base}_multimap_1.fastq
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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76 --fastqfile2 ${input_base}_multimap_2.fastq
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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77 --alignment_bam ${input_base}_unique.bam
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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78 --cpus "\${GALAXY_SLOTS:-4}"
89e05f831259 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
artbio
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79 --pairedend TRUE &&
0
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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80 #end if
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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81 cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular &&
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82 cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular &&
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83 cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular
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84 ]]></command>
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85 <!-- basic error handling -->
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86 <inputs>
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87 <conditional name="seq_method">
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88 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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89 <option selected="True" value="single-read">Single-read sequencing</option>
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90 <option value="paired-end">Paired-end sequencing</option>
5
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91 <option value="paired_collection">Paired-end Dataset Collection</option>
0
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92 </param>
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93 <when value="single-read">
5
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94 <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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95 </when>
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96 <when value="paired-end">
5
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97 <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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98 <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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99 </when>
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100 <when value="paired_collection">
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101 <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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102 </when>
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103 </conditional>
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104 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />
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105 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
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106 </inputs>
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107
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108 <outputs>
2
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109 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb" />
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110 <data format="tabular" name="class_fraction_counts" label="RepEnrich on ${on_string}: class fraction counts" from_work_dir="class_fraction_counts.tabular" />
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111 <data format="tabular" name="family_fraction_counts" label="RepEnrich on ${on_string}: family fraction counts" from_work_dir="family_fraction_counts.tabular" />
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112 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular" />
0
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113 </outputs>
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114
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115 <tests>
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116 <test>
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117 <param name="seq_method_list" value="single-read"/>
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118 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/>
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119 <param name="genome" value="chrM.fa" ftype="fasta"/>
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120 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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121 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
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122 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
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123 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
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124 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
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125 </test>
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126 <test>
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127 <param name="seq_method_list" value="paired-end"/>
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128 <param name="input_fastq" value="Samp_L.fastq" ftype="fastq"/>
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129 <param name="input2_fastq" value="Samp_R.fastq" ftype="fastq"/>
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130 <param name="genome" value="chrM.fa" ftype="fasta"/>
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131 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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132 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
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133 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
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134 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
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135 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
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136 </test>
4
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137 <test>
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138 <param name="seq_method_list" value="single-read"/>
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139 <param name="input_fastq" value="Samp.fastq.gz" ftype="fastq.gz"/>
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140 <param name="genome" value="chrM.fa" ftype="fasta"/>
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141 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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142 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
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143 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
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144 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
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145 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
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146 </test>
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147 <test>
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148 <param name="seq_method_list" value="paired-end"/>
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149 <param name="input_fastq" value="Samp_L.fastq.gz" ftype="fastq.gz"/>
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150 <param name="input2_fastq" value="Samp_R.fastq.gz" ftype="fastq.gz"/>
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151 <param name="genome" value="chrM.fa" ftype="fasta"/>
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152 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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153 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
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154 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
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155 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
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156 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
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157 </test>
0
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158 </tests>
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159
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160 <help>
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161
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162 **What it does**
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163
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164 Reads are mapped to the genome using the Bowtie1 aligner. Reads mapping uniquely to the genome are assigned to subfamilies of repetitive elements based on their degree of overlap to RepeatMasker annotated genomic instances of each repetitive element subfamily. Reads mapping to multiple locations are separately mapped to repetitive element assemblies – referred to as repetitive element psuedogenomes – built from RepeatMasker annotated genomic instances of repetitive element subfamilies. RepEnrich then return tables of counts merged from both strategies, that can be further processed in statistical analysis for differential expression. For detailed information see the `original publication`_.
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165
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166 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583
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167
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168 **Inputs**
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169
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170 *Reference genome* : reference genome in fasta format
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171
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172 *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format.
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173
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174 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
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175
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176 This file looks like:
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177
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178 <![CDATA[
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179
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180 SW perc perc perc query position in query matching repeat position in repeat
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181
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182 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID
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183
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184 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486
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185
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186 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487
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187
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188 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488
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189
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190 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489
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191
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192 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490
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193
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194 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491
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195
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196 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492
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197
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198 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493
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199
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200 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494
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202 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495
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204 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496
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206 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497
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208 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498
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209
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210 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499
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211
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212 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500
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213
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214 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501
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215
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216 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502
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217
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218 ]]>
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219
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220 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons)
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221
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222 **Outputs**
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223
1
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224 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format,
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225 for further statistical tests differential expression analysis or graphics.
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226
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227 The "aligned_reads.tab" output file contains a single value corresponding to the number of reads that were aligned to
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228 transposons. This value is used in downstream analysis by the edger-repenrich tool.
0
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229
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230 **RepEnrich**
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231
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232 This Galaxy tool is a wrapper of the RepEnrich tool by steven_criscione@brown.edu et al. whose code and manual are available in `GitHub`_.
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233
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234 .. _GitHub: https://github.com/nskvir/RepEnrich
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235
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236 Python scripts RepEnrich.py and RepEnrich_setup.py have been adapted to python 3. Note that sorting of Fraction counts, Family fraction counts and Class fraction counts is different with this Galaxy wrapper or with RepEnrich as found in the `RepEnrich code repository`_. However, this different sorting does not affect subsequent statistical analyses
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237
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238 .. _RepEnrich code repository: https://github.com/nskvir/RepEnrich
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239
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240 **Execution time**
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241
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242 .. class:: warningmark
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243
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244 This tool includes steps to index the reference genome, index repeat sequences and align reads to these indexes. Therefore the run time may be **long to very long**.
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245
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246 .. class:: infomark
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247
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248 For more information on the tools, or giving us feedback, please visit our `code repository`_.
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250 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/
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251 .. _ARTbio team: http://artbio.fr
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253 </help>
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255 <citations>
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256 <citation type="doi">10.1186/1471-2164-15-583</citation>
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257 </citations>
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258 </tool>