Mercurial > repos > artbio > repenrich
annotate repenrich.xml @ 1:51b4590a972d draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 98f4b00d71cbc2dd15fc633a6cc3246235308e46
| author | artbio |
|---|---|
| date | Mon, 18 Sep 2017 17:22:07 -0400 |
| parents | f6f0f1e5e940 |
| children | 15e3e29f310e |
| rev | line source |
|---|---|
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1
51b4590a972d
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 98f4b00d71cbc2dd15fc633a6cc3246235308e46
artbio
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changeset
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1 <tool id="repenrich" name="RepEnrich" version="1.4.1"> |
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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
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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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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:
diff
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 $seq_method.seq_method_list == "paired-end": |
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f6f0f1e5e940
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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changeset
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19 ln -f -s '$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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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:
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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:
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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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diff
changeset
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26 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && |
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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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27 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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28 #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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29 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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30 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
parents:
diff
changeset
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31 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && |
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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 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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33 #end if |
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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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34 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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changeset
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35 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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36 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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changeset
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37 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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38 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
parents:
diff
changeset
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39 #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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40 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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changeset
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41 #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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42 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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changeset
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43 #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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44 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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45 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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46 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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47 ]]></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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48 <!-- 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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49 <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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50 <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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51 <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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52 <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
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53 <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
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changeset
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54 </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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55 <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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56 <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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changeset
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57 </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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58 <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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59 <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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60 <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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61 </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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changeset
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62 </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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63 <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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changeset
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64 <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
parents:
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65 </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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66 |
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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 <outputs> |
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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 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="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
parents:
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changeset
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69 </data> |
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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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70 <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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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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71 </data> |
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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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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> |
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74 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular"> |
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75 </data> |
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76 </outputs> |
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77 |
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78 <tests> |
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79 <test> |
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80 <param name="seq_method_list" value="single-read"/> |
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81 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/> |
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82 <param name="genome" value="chrM.fa" ftype="fasta"/> |
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83 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> |
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84 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/> |
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85 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/> |
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86 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> |
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87 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/> |
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88 </test> |
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89 <test> |
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90 <param name="seq_method_list" value="paired-end"/> |
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91 <param name="input_fastq" value="Samp_L.fastq" ftype="fastq"/> |
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92 <param name="input2_fastq" value="Samp_R.fastq" ftype="fastq"/> |
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93 <param name="genome" value="chrM.fa" ftype="fasta"/> |
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94 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> |
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95 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/> |
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96 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/> |
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97 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/> |
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98 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/> |
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99 </test> |
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100 </tests> |
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101 |
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102 <help> |
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103 |
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104 **What it does** |
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105 |
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106 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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107 |
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108 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583 |
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109 |
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110 **Inputs** |
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111 |
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112 *Reference genome* : reference genome in fasta format |
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113 |
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114 *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format. |
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115 |
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116 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html |
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117 |
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118 This file looks like: |
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119 |
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120 <![CDATA[ |
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121 |
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122 SW perc perc perc query position in query matching repeat position in repeat |
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123 |
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124 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID |
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125 |
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126 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486 |
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127 |
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128 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487 |
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129 |
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130 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488 |
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131 |
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132 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489 |
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133 |
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134 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490 |
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135 |
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136 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491 |
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137 |
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138 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492 |
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139 |
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140 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493 |
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141 |
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142 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494 |
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143 |
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144 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495 |
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145 |
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146 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496 |
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147 |
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148 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497 |
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150 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498 |
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151 |
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152 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499 |
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153 |
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154 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500 |
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156 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501 |
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157 |
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158 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502 |
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159 |
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160 ]]> |
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161 |
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162 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons) |
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163 |
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164 **Outputs** |
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165 |
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1
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166 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format, |
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167 for further statistical tests differential expression analysis or graphics. |
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168 |
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169 The "aligned_reads.tab" output file contains a single value corresponding to the number of reads that were aligned to |
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170 transposons. This value is used in downstream analysis by the edger-repenrich tool. |
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171 |
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172 **RepEnrich** |
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173 |
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174 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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175 |
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176 .. _GitHub: https://github.com/nskvir/RepEnrich |
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177 |
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178 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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179 |
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180 .. _RepEnrich code repository: https://github.com/nskvir/RepEnrich |
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181 |
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182 **Execution time** |
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183 |
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184 .. class:: warningmark |
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185 |
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186 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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187 |
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188 .. class:: infomark |
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189 |
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190 For more information on the tools, please visit our `code repository`_. |
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191 |
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192 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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193 |
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194 This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_. |
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195 |
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196 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/ |
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197 .. _ARTbio team: http://artbio.fr |
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198 .. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics |
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199 |
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200 </help> |
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201 |
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202 <citations> |
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203 <citation type="doi">10.1186/1471-2164-15-583</citation> |
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204 </citations> |
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205 </tool> |