Mercurial > repos > artbio > repenrich
diff repenrich.xml @ 11:6bba3e33c2e7 draft
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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--- a/repenrich.xml Tue Feb 05 17:20:55 2019 -0500 +++ b/repenrich.xml Sat Mar 09 22:32:46 2024 +0000 @@ -1,11 +1,9 @@ -<tool id="repenrich" name="RepEnrich" version="1.6.1"> +<tool id="repenrich" name="RepEnrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>Repeat Element Profiling</description> - <requirements> - <requirement type="package" version="1.2.0">bowtie</requirement> - <requirement type="package" version="0.1.19">samtools</requirement> - <requirement type="package" version="2.20.1">bedtools</requirement> - <requirement type="package" version="1.69">biopython</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> @@ -55,11 +53,8 @@ echo -e "# Total reads aligned to repeated sequences\n" > bowtie_aligned.numb && echo \$((\$TOTAL-\$NONALIGNED)) >> bowtie_aligned.numb && #end if - samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam && - samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted && - mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam && + samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' && samtools index ${input_base}_unique.bam && - rm ${input_base}_unique.sam && #if $seq_method.seq_method_list == "single-read": 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}" && #else: