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comparison repenrich.xml @ 12:89e05f831259 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 212b838f614f1f7b8e770473c026d9c1180722df
author artbio
date Mon, 18 Mar 2024 09:39:44 +0000
parents 6bba3e33c2e7
children 530626b0757c
comparison
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11:6bba3e33c2e7 12:89e05f831259
28 ln -f -s '$seq_method.input_fastq.reverse' '${input_base}_2.fastq' && 28 ln -f -s '$seq_method.input_fastq.reverse' '${input_base}_2.fastq' &&
29 #end if 29 #end if
30 #else: 30 #else:
31 #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): 31 #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
32 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' && 32 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
33 gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' && 33 gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' &&
34 #else: 34 #else:
35 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' && 35 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
36 ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' && 36 ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' &&
37 #end if 37 #end if
38 #end if 38 #end if
39
40 ln -f -s '$genome' '${baseReference}.fa' && 39 ln -f -s '$genome' '${baseReference}.fa' &&
41 bowtie-build '$genome' ${baseReference} && 40 bowtie-build '$genome' ${baseReference} &&
42 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && 41 python $__tool_directory__/RepEnrich_setup.py
42 --annotation_file $repeatmasker
43 --genomefasta ${baseReference}.fa
44 --setup_folder setup_folder_${baseReference} &&
43 #if $seq_method.seq_method_list == "single-read": 45 #if $seq_method.seq_method_list == "single-read":
44 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 && 46 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
45 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && 47 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
46 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && 48 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
47 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && 49 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
54 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && 56 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
55 #end if 57 #end if
56 samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' && 58 samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' &&
57 samtools index ${input_base}_unique.bam && 59 samtools index ${input_base}_unique.bam &&
58 #if $seq_method.seq_method_list == "single-read": 60 #if $seq_method.seq_method_list == "single-read":
59 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}" && 61 python $__tool_directory__/RepEnrich.py
62 --annotation_file $repeatmasker
63 --outputfolder ${input_base}
64 --outputprefix ${input_base}
65 --setup_folder setup_folder_${baseReference}
66 --fastqfile ${input_base}_multimap.fastq
67 --alignment_bam ${input_base}_unique.bam
68 --cpus "\${GALAXY_SLOTS:-4}" &&
60 #else: 69 #else:
61 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 && 70 python $__tool_directory__/RepEnrich.py
71 --annotation_file $repeatmasker
72 --outputfolder ${input_base}
73 --outputprefix ${input_base}
74 --setup_folder setup_folder_${baseReference}
75 --fastqfile ${input_base}_multimap_1.fastq
76 --fastqfile2 ${input_base}_multimap_2.fastq
77 --alignment_bam ${input_base}_unique.bam
78 --cpus "\${GALAXY_SLOTS:-4}"
79 --pairedend TRUE &&
62 #end if 80 #end if
63 cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular && 81 cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular &&
64 cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular && 82 cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular &&
65 cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular 83 cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular
66 ]]></command> 84 ]]></command>
225 243
226 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**. 244 This tool includes steps to index the reference genome, index repeat sequences and align reads to these indexes. Therefore the run time may be **long to very long**.
227 245
228 .. class:: infomark 246 .. class:: infomark
229 247
230 For more information on the tools, please visit our `code repository`_. 248 For more information on the tools, or giving us feedback, please visit our `code repository`_.
231
232 If you would like to give us feedback or you run into any trouble, please send an email to artbio.ibps@gmail.com
233
234 This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_.
235 249
236 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/ 250 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/
237 .. _ARTbio team: http://artbio.fr 251 .. _ARTbio team: http://artbio.fr
238 .. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics
239 252
240 </help> 253 </help>
241 254
242 <citations> 255 <citations>
243 <citation type="doi">10.1186/1471-2164-15-583</citation> 256 <citation type="doi">10.1186/1471-2164-15-583</citation>