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annotate repenrich.xml @ 11:6bba3e33c2e7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
author artbio
date Sat, 09 Mar 2024 22:32:46 +0000
parents 6f4143893463
children 89e05f831259
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11
6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
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1 <tool id="repenrich" name="RepEnrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>Repeat Element Profiling</description>
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3 <macros>
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4 <import>macros.xml</import>
6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
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5 </macros>
6bba3e33c2e7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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12 #set input_base = 'Sample'
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13 #set baseReference = 'Genome'
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d1f7ab78f7b5 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 2066f507880250c0093e7353e7c18910c002b05f
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15 ## uncompress fastq.gz or fastqsanger.gz if needed
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16 #if $seq_method.seq_method_list == "single-read":
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17 #if $seq_method.input_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
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18 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
4
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19 #else:
5
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20 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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21 #end if
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22 #elif $seq_method.seq_method_list == 'paired_collection':
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23 #if $seq_method.input_fastq.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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24 gunzip < '$seq_method.input_fastq.forward' > '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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25 gunzip < '$seq_method.input_fastq.reverse' > '${input_base}_2.fastq' &&
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26 #else:
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27 ln -f -s '$seq_method.input_fastq.forward' '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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28 ln -f -s '$seq_method.input_fastq.reverse' '${input_base}_2.fastq' &&
4
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29 #end if
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30 #else:
5
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31 #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"):
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32 gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' &&
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33 gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' &&
4
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34 #else:
5
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35 ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' &&
02a8941da83b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 1b8b12d9df3ebb8e36c098e4c2f200b93ed34f10
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36 ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' &&
4
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37 #end if
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38 #end if
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39
0
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40 ln -f -s '$genome' '${baseReference}.fa' &&
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41 bowtie-build '$genome' ${baseReference} &&
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42 python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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43 #if $seq_method.seq_method_list == "single-read":
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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 &&
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45 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
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46 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
2
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47 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
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48 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
0
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49 #else:
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50 bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq -1 ${input_base}.fastq -2 ${input_base}_2.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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51 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
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52 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
2
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53 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
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54 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
0
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55 #end if
11
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56 samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' &&
0
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57 samtools index ${input_base}_unique.bam &&
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58 #if $seq_method.seq_method_list == "single-read":
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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}" &&
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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60 #else:
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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 &&
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62 #end if
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63 cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular &&
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64 cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular &&
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65 cp $input_base/${input_base}_fraction_counts.txt fraction_counts.tabular
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66 ]]></command>
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67 <!-- basic error handling -->
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68 <inputs>
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69 <conditional name="seq_method">
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70 <param help="Paired-end or single-read sequencing" label="Sequencing method" name="seq_method_list" type="select">
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71 <option selected="True" value="single-read">Single-read sequencing</option>
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72 <option value="paired-end">Paired-end sequencing</option>
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73 <option value="paired_collection">Paired-end Dataset Collection</option>
0
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74 </param>
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75 <when value="single-read">
5
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76 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="Single-reads" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
0
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77 </when>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
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78 <when value="paired-end">
5
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79 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="1st paired-end sequencing dataset" name="input_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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80 <param format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="2nd paired-end sequencing dataset" name="input2_fastq" type="data" help="accepted formats: fastq, fastqsanger" />
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81 </when>
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82 <when value="paired_collection">
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83 <param name="input_fastq" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" type="data_collection" collection_type="paired" label="Paired Collection" help="Must be of datatype &quot;fastqsanger&quot; or &quot;fasta&quot;" />
0
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84 </when>
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85 </conditional>
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86 <param format="fasta" label="Reference genome in fasta format" name="genome" type="data" />
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87 <param format="txt" label="RepeatMasker description file" name="repeatmasker" type="data" help="see help section"/>
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88 </inputs>
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89
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90 <outputs>
2
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91 <data format="tabular" name="bowtie_alignments" label="RepEnrich on ${on_string}: reads aligned" from_work_dir="bowtie_aligned.numb" />
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92 <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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93 <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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94 <data format="tabular" name="fraction_counts" label="RepEnrich on ${on_string}: fraction counts" from_work_dir="fraction_counts.tabular" />
0
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95 </outputs>
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96
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97 <tests>
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98 <test>
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99 <param name="seq_method_list" value="single-read"/>
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100 <param name="input_fastq" value="Samp.fastq" ftype="fastq"/>
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101 <param name="genome" value="chrM.fa" ftype="fasta"/>
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102 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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103 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
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104 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
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105 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
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106 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
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107 </test>
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108 <test>
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109 <param name="seq_method_list" value="paired-end"/>
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110 <param name="input_fastq" value="Samp_L.fastq" ftype="fastq"/>
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111 <param name="input2_fastq" value="Samp_R.fastq" ftype="fastq"/>
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112 <param name="genome" value="chrM.fa" ftype="fasta"/>
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113 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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114 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
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115 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
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116 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
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117 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
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118 </test>
4
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119 <test>
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120 <param name="seq_method_list" value="single-read"/>
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121 <param name="input_fastq" value="Samp.fastq.gz" ftype="fastq.gz"/>
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122 <param name="genome" value="chrM.fa" ftype="fasta"/>
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123 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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124 <output name="bowtie_alignments" file="aligned_reads.tab" ftype="tabular"/>
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125 <output name="class_fraction_counts" file="Samp_class_fraction_counts.tabular" ftype="tabular"/>
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126 <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/>
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127 <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/>
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128 </test>
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129 <test>
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130 <param name="seq_method_list" value="paired-end"/>
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131 <param name="input_fastq" value="Samp_L.fastq.gz" ftype="fastq.gz"/>
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132 <param name="input2_fastq" value="Samp_R.fastq.gz" ftype="fastq.gz"/>
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133 <param name="genome" value="chrM.fa" ftype="fasta"/>
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134 <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/>
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135 <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/>
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136 <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/>
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137 <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/>
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138 <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/>
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139 </test>
0
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140 </tests>
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141
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142 <help>
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143
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144 **What it does**
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145
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146 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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147
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148 .. _original publication: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-583
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149
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150 **Inputs**
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151
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152 *Reference genome* : reference genome in fasta format
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153
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154 *Sequencing dataset*: Single-reads or Paired-end sequencing datasets in fastq format.
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155
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156 *RepeatMasker description file*: a txt repeatmasker file which can be downloaded from http://www.repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
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157
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158 This file looks like:
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159
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160 <![CDATA[
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162 SW perc perc perc query position in query matching repeat position in repeat
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164 score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID
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166 16 20.2 5.9 0.0 chrM 1211 1261 (18263) + (TTTTA)n Simple_repeat 1 54 (0) 84486
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168 13 23.9 2.2 2.2 chrM 2014 2059 (17465) + (TTA)n Simple_repeat 1 46 (0) 84487
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170 24 18.8 5.3 2.6 chrM 3924 3999 (15525) + (TAT)n Simple_repeat 1 78 (0) 84488
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172 18 4.5 0.0 0.0 chrM 5961 5983 (13541) + (AT)n Simple_repeat 1 23 (0) 84489
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174 13 25.9 4.0 4.0 chrM 6247 6320 (13204) + (ATTTAT)n Simple_repeat 1 74 (0) 84490
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176 11 14.6 7.5 2.4 chrM 8783 8822 (10702) + (CTAATT)n Simple_repeat 1 42 (0) 84491
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178 17 19.0 0.0 8.6 chrM 9064 9126 (10398) + A-rich Low_complexity 1 58 (0) 84492
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180 13 21.0 5.9 1.9 chrM 11723 11773 (7751) + (ATA)n Simple_repeat 1 53 (0) 84493
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182 66 20.4 12.3 12.3 chrM 12823 13001 (6523) C LSU-rRNA_Cel rRNA (1) 2431 2253 84494
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184 16 16.6 0.0 2.9 chrM 14361 14396 (5128) + (ATT)n Simple_repeat 1 35 (0) 84495
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186 44 2.4 0.0 0.0 chrM 15966 16007 (3517) + (TA)n Simple_repeat 1 42 (0) 84496
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188 35 5.3 0.0 0.0 chrM 16559 16597 (2927) + (AT)n Simple_repeat 1 39 (0) 84497
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190 36 2.9 0.0 0.0 chrM 16922 16956 (2568) + (AT)n Simple_repeat 1 35 (0) 84498
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192 37 0.0 0.0 0.0 chrM 17040 17071 (2453) + (TA)n Simple_repeat 1 32 (0) 84499
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194 20 4.3 0.0 0.0 chrM 17417 17440 (2084) + (T)n Simple_repeat 1 24 (0) 84500
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196 31 6.9 6.3 1.5 chrM 17451 17513 (2011) + (TA)n Simple_repeat 1 66 (0) 84501
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198 26 17.0 0.0 0.0 chrM 19469 19514 (10) + A-rich Low_complexity 1 46 (0) 84502
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200 ]]>
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202 Users may filter this file so that it contains only desired items (for instance only satellites, repeats and transposons)
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204 **Outputs**
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205
1
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206 (1) Fraction counts, (2) Family fraction counts and (3) Class fraction counts are returned in tabular format,
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207 for further statistical tests differential expression analysis or graphics.
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208
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209 The "aligned_reads.tab" output file contains a single value corresponding to the number of reads that were aligned to
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210 transposons. This value is used in downstream analysis by the edger-repenrich tool.
0
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211
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212 **RepEnrich**
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213
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214 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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215
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216 .. _GitHub: https://github.com/nskvir/RepEnrich
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217
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218 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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219
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220 .. _RepEnrich code repository: https://github.com/nskvir/RepEnrich
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221
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222 **Execution time**
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223
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224 .. class:: warningmark
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225
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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**.
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227
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228 .. class:: infomark
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229
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230 For more information on the tools, please visit our `code repository`_.
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231
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232 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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233
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234 This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_.
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235
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236 .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/
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237 .. _ARTbio team: http://artbio.fr
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238 .. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics
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239
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240 </help>
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241
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242 <citations>
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243 <citation type="doi">10.1186/1471-2164-15-583</citation>
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244 </citations>
f6f0f1e5e940 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 61e203df0be5ed877ff92b917c7cde6eeeab8310
artbio
parents:
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245 </tool>