Mercurial > repos > artbio > repenrich
annotate repenrich.xml @ 2:15e3e29f310e draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
| author | artbio |
|---|---|
| date | Tue, 19 Sep 2017 17:23:15 -0400 |
| parents | 51b4590a972d |
| children | 1c9810ba0638 |
| rev | line source |
|---|---|
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2
15e3e29f310e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents:
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changeset
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1 <tool id="repenrich" name="RepEnrich" version="1.4.2"> |
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0
f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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2 <description>Repeat Element Profiling</description> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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changeset
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3 <requirements> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff
changeset
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4 <requirement type="package" version="1.2.0">bowtie</requirement> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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5 <requirement type="package" version="0.1.19">samtools</requirement> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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6 <requirement type="package" version="2.20.1">bedtools</requirement> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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7 <requirement type="package" version="1.69">biopython</requirement> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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8 </requirements> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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9 <stdio> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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10 <exit_code range="1:" level="fatal" description="Tool exception" /> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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changeset
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11 </stdio> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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12 <command detect_errors="exit_code"><![CDATA[ |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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13 #import re |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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14 #set input_base = 'Sample' |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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15 #set baseReference = 'Genome' |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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16 ln -f -s '$genome' '${baseReference}.fa' && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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17 ln -f -s '$input_fastq' '${input_base}.fastq' && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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18 #if $seq_method.seq_method_list == "paired-end": |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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19 ln -f -s '$input2_fastq' '${input_base}_2.fastq' && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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20 #end if |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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21 bowtie-build '$genome' ${baseReference} && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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22 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff
changeset
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23 #if $seq_method.seq_method_list == "single-read": |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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24 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 && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff
changeset
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25 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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26 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && |
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2
15e3e29f310e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
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diff
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27 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && |
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15e3e29f310e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
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1
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changeset
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28 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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29 #else: |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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30 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 && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff
changeset
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31 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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32 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && |
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2
15e3e29f310e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
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1
diff
changeset
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33 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && |
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15e3e29f310e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
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1
diff
changeset
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34 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && |
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0
f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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35 #end if |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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36 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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37 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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38 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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39 samtools index ${input_base}_unique.bam && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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40 rm ${input_base}_unique.sam && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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41 #if $seq_method.seq_method_list == "single-read": |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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42 python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --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
artbio
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diff
changeset
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43 #else: |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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44 python $__tool_directory__/RepEnrich.py $repeatmasker ${input_base} ${input_base} setup_folder_${baseReference} ${input_base}_multimap_1.fastq --fastqfile2 ${input_base}_multimap_2.fastq ${input_base}_unique.bam --cpus "\${GALAXY_SLOTS:-4}" --pairedend TRUE && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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45 #end if |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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46 cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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47 cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular && |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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48 cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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49 ]]></command> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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50 <!-- basic error handling --> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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51 <inputs> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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52 <conditional name="seq_method"> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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diff
changeset
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53 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select"> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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54 <option selected="True" value="single-read">Single-read sequencing</option> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff
changeset
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55 <option value="paired-end">Paired-end sequencing</option> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff
changeset
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56 </param> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
diff
changeset
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57 <when value="single-read"> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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58 <param format="fastq,fastqsanger" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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59 </when> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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changeset
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60 <when value="paired-end"> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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61 <param format="fastq,fastqsanger" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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62 <param format="fastq,fastqsanger" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" /> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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changeset
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63 </when> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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64 </conditional> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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65 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" /> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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66 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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67 </inputs> |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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68 |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
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69 <outputs> |
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2
15e3e29f310e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents:
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70 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb" /> |
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15e3e29f310e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit c89c33e5ea8fc63f3ea5c0f66ebc5fa822ac734b
artbio
parents:
1
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71 <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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72 <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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73 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular" /> |
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74 </outputs> |
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75 |
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76 <tests> |
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77 <test> |
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78 <param name="seq_method_list" value="single-read"/> |
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79 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/> |
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80 <param name="genome" value="chrM.fa" ftype="fasta"/> |
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81 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> |
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82 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/> |
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83 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/> |
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84 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> |
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85 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/> |
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86 </test> |
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87 <test> |
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88 <param name="seq_method_list" value="paired-end"/> |
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89 <param name="input_fastq" value="Samp_L.fastq" ftype="fastq"/> |
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90 <param name="input2_fastq" value="Samp_R.fastq" ftype="fastq"/> |
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91 <param name="genome" value="chrM.fa" ftype="fasta"/> |
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92 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> |
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93 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/> |
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94 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/> |
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95 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/> |
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96 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/> |
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97 </test> |
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98 </tests> |
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99 |
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100 <help> |
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101 |
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102 **What it does** |
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103 |
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104 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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105 |
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106 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583 |
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107 |
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108 **Inputs** |
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109 |
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110 *Reference genome* : reference genome in fasta format |
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111 |
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112 *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format. |
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113 |
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114 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html |
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115 |
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116 This file looks like: |
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117 |
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118 <![CDATA[ |
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119 |
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120 SW perc perc perc query position in query matching repeat position in repeat |
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121 |
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122 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID |
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123 |
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124 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486 |
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125 |
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126 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487 |
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127 |
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128 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488 |
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129 |
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130 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489 |
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131 |
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132 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490 |
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133 |
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134 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491 |
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135 |
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136 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492 |
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137 |
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138 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493 |
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139 |
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140 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494 |
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141 |
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142 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495 |
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143 |
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144 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496 |
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145 |
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146 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497 |
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147 |
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148 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498 |
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149 |
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150 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499 |
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151 |
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152 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500 |
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153 |
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154 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501 |
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155 |
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156 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502 |
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157 |
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158 ]]> |
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159 |
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160 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons) |
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161 |
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162 **Outputs** |
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163 |
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1
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164 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format, |
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165 for further statistical tests differential expression analysis or graphics. |
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166 |
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167 The "aligned_reads.tab" output file contains a single value corresponding to the number of reads that were aligned to |
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168 transposons. This value is used in downstream analysis by the edger-repenrich tool. |
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169 |
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170 **RepEnrich** |
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171 |
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172 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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173 |
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174 .. _GitHub: https://github.com/nskvir/RepEnrich |
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175 |
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176 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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177 |
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178 .. _RepEnrich code repository: https://github.com/nskvir/RepEnrich |
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179 |
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180 **Execution time** |
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181 |
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182 .. class:: warningmark |
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183 |
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184 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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185 |
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186 .. class:: infomark |
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187 |
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188 For more information on the tools, please visit our `code repository`_. |
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189 |
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190 If you would like to give us feedback or you run into any trouble, please send an email to artbio.ibps@gmail.com |
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191 |
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192 This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_. |
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193 |
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194 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/ |
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195 .. _ARTbio team: http://artbio.fr |
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196 .. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics |
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197 |
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198 </help> |
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199 |
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200 <citations> |
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201 <citation type="doi">10.1186/1471-2164-15-583</citation> |
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202 </citations> |
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203 </tool> |