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comparison 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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10:6f4143893463 11:6bba3e33c2e7
1 <tool id="repenrich" name="RepEnrich" version="1.6.1"> 1 <tool id="repenrich" name="RepEnrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Repeat Element Profiling</description> 2 <description>Repeat Element Profiling</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="1.2.0">bowtie</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="0.1.19">samtools</requirement> 5 </macros>
6 <requirement type="package" version="2.20.1">bedtools</requirement> 6 <expand macro="requirements"/>
7 <requirement type="package" version="1.69">biopython</requirement>
8 </requirements>
9 <stdio> 7 <stdio>
10 <exit_code range="1:" level="fatal" description="Tool exception" /> 8 <exit_code range="1:" level="fatal" description="Tool exception" />
11 </stdio> 9 </stdio>
12 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
13 #import re 11 #import re
53 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && 51 TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) &&
54 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) && 52 NONALIGNED=\$(grep 'reads that failed to align:' bowtie_alignments.txt | cut -d ' ' -f 7) &&
55 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && 53 echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb &&
56 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && 54 echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb &&
57 #end if 55 #end if
58 samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && 56 samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' &&
59 samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted &&
60 mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam &&
61 samtools index ${input_base}_unique.bam && 57 samtools index ${input_base}_unique.bam &&
62 rm ${input_base}_unique.sam &&
63 #if $seq_method.seq_method_list == "single-read": 58 #if $seq_method.seq_method_list == "single-read":
64 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}" && 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}" &&
65 #else: 60 #else:
66 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 && 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 &&
67 #end if 62 #end if