Mercurial > repos > drosofff > repenrich
annotate repenrich.xml @ 6:55a849141d64 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
| author | drosofff |
|---|---|
| date | Tue, 30 May 2017 19:52:53 -0400 |
| parents | 15f264b2a6e3 |
| children | 895c91bbaffe |
| rev | line source |
|---|---|
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6
55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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1 <tool id="repenrich" name="RepEnrich" version="1.2.0"> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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2 <description>Repeat Element Profiling</description> |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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3 <requirements> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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4 <requirement type="package" version="1.2.0">bowtie</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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5 <requirement type="package" version="0.1.19">samtools</requirement> |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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6 <requirement type="package" version="2.20.1">bedtools</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit d5ebd581fa3a22ca61ce07a31c01bb70610fbcf5
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7 <requirement type="package" version="1.69">biopython</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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8 </requirements> |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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9 <stdio> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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10 <exit_code range="1:" level="fatal" description="Tool exception" /> |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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11 </stdio> |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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12 <command detect_errors="exit_code"><![CDATA[ |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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13 #import re |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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14 #set input_base = 'Sample' |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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15 #set baseReference = 'Genome' |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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16 ln -f -s '$genome' '${baseReference}.fa' && |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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17 ln -f -s '$input_fastq' '${input_base}.fastq' && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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18 #if $seq_method.seq_method_list == "paired-end": |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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19 ln -f -s '$input2_fastq' '${input_base}_2.fastq' && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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20 #end if |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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21 bowtie-build '$genome' ${baseReference} && |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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22 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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23 #if $seq_method.seq_method_list == "single-read": |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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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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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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25 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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26 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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27 echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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28 #else: |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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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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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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30 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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31 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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32 echo \$((\$TOTAL-\$NONALIGNED)) > bowtie_aligned.numb && |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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33 #end if |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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34 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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35 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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36 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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37 samtools index ${input_base}_unique.bam && |
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041de602103e
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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38 rm ${input_base}_unique.sam && |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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39 #if $seq_method.seq_method_list == "single-read": |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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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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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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41 #else: |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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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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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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43 #end if |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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44 cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular && |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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45 cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular && |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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46 cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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47 ]]></command> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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48 <!-- basic error handling --> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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49 <inputs> |
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50 <conditional name="seq_method"> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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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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52 <option selected="True" value="single-read">Single-read sequencing</option> |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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53 <option value="paired-end">Paired-end sequencing</option> |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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54 </param> |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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55 <when value="single-read"> |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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57 </when> |
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55a849141d64
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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58 <when value="paired-end"> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
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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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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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61 </when> |
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62 </conditional> |
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63 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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64 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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65 </inputs> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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66 |
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67 <outputs> |
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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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69 </data> |
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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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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71 </data> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ef0b32c10d178e61faf9042bc5e0d3cc66a10729
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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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6
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76 <data format="tabular" name="bowtieoutput" label="bowtie aligments" from_work_dir="bowtie_alignments.txt"> |
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77 </data> |
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78 </outputs> |
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0
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79 |
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80 <tests> |
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81 <test> |
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6
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82 <param name="seq_method_list" value="single-read"/> |
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83 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/> |
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84 <param name="genome" value="chrM.fa" ftype="fasta"/> |
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85 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> |
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86 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/> |
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87 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/> |
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88 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> |
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89 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/> |
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90 </test> |
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91 </tests> |
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92 |
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93 <help> |
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94 |
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95 **What it does** |
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96 |
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97 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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98 |
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99 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583 |
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100 |
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101 **Inputs** |
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102 |
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103 *Reference genome* : reference genome in fasta format |
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104 |
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105 *Sequencing dataset*: Single-reads sequencing dataset. Paired-end sequencing dataset in not implemented yet |
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106 |
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107 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html |
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108 |
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109 This file looks like: |
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110 |
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111 <![CDATA[ |
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112 |
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113 SW perc perc perc query position in query matching repeat position in repeat |
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114 |
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115 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID |
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116 |
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117 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486 |
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118 |
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119 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487 |
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120 |
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121 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488 |
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122 |
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123 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489 |
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124 |
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125 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490 |
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126 |
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127 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491 |
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128 |
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129 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492 |
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130 |
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131 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493 |
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132 |
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133 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494 |
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134 |
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135 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495 |
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136 |
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137 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496 |
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138 |
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139 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497 |
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140 |
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141 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498 |
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142 |
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143 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499 |
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144 |
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145 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500 |
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146 |
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147 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501 |
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148 |
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149 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502 |
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151 ]]> |
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153 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons) |
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155 **Outputs** |
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157 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format, for further statistical tests differential expression analysis or graphics |
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158 |
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159 **RepEnrich** |
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161 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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162 |
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163 .. _GitHub: https://github.com/nskvir/RepEnrich |
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165 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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166 |
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167 .. _RepEnrich code repository: https://github.com/nskvir/RepEnrich |
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169 **Execution time** |
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171 .. class:: warningmark |
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172 |
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173 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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174 |
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175 .. class:: infomark |
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177 For more information on the tools, please visit our `code repository`_. |
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178 |
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179 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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181 This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_. |
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183 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/ |
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184 .. _ARTbio team: http://artbio.fr |
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185 .. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics |
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187 </help> |
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188 |
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189 <citations> |
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190 <citation type="doi">10.1186/1471-2164-15-583</citation> |
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191 </citations> |
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192 </tool> |