Mercurial > repos > artbio > repenrich
diff repenrich.xml @ 12:89e05f831259 draft
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 |
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--- a/repenrich.xml Sat Mar 09 22:32:46 2024 +0000 +++ b/repenrich.xml Mon Mar 18 09:39:44 2024 +0000 @@ -30,16 +30,18 @@ #else: #if $seq_method.input2_fastq.is_of_type("fastq.gz", "fastqsanger.gz"): gunzip < '$seq_method.input_fastq' > '${input_base}.fastq' && - gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' && + gunzip < '$seq_method.input2_fastq' > '${input_base}_2.fastq' && #else: ln -f -s '$seq_method.input_fastq' '${input_base}.fastq' && ln -f -s '$seq_method.input2_fastq' '${input_base}_2.fastq' && #end if #end if - ln -f -s '$genome' '${baseReference}.fa' && bowtie-build '$genome' ${baseReference} && - python $__tool_directory__/RepEnrich_setup.py $repeatmasker ${baseReference}.fa setup_folder_${baseReference} && + python $__tool_directory__/RepEnrich_setup.py + --annotation_file $repeatmasker + --genomefasta ${baseReference}.fa + --setup_folder setup_folder_${baseReference} && #if $seq_method.seq_method_list == "single-read": bowtie $baseReference -p \${GALAXY_SLOTS:-4} -t -m 1 -S --max ${input_base}_multimap.fastq ${input_base}.fastq ${input_base}_unique.sam 2>bowtie_alignments.txt && TOTAL=\$(grep 'reads processed:' bowtie_alignments.txt | cut -d ' ' -f 4) && @@ -56,9 +58,25 @@ samtools view -@ \${GALAXY_SLOTS:-4} -bS '${input_base}_unique.sam' | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '${input_base}_unique.bam' && samtools index ${input_base}_unique.bam && #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}" && + python $__tool_directory__/RepEnrich.py + --annotation_file $repeatmasker + --outputfolder ${input_base} + --outputprefix ${input_base} + --setup_folder setup_folder_${baseReference} + --fastqfile ${input_base}_multimap.fastq + --alignment_bam ${input_base}_unique.bam + --cpus "\${GALAXY_SLOTS:-4}" && #else: - 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 && + python $__tool_directory__/RepEnrich.py + --annotation_file $repeatmasker + --outputfolder ${input_base} + --outputprefix ${input_base} + --setup_folder setup_folder_${baseReference} + --fastqfile ${input_base}_multimap_1.fastq + --fastqfile2 ${input_base}_multimap_2.fastq + --alignment_bam ${input_base}_unique.bam + --cpus "\${GALAXY_SLOTS:-4}" + --pairedend TRUE && #end if cp $input_base/${input_base}_class_fraction_counts.txt class_fraction_counts.tabular && cp $input_base/${input_base}_family_fraction_counts.txt family_fraction_counts.tabular && @@ -227,15 +245,10 @@ .. class:: infomark -For more information on the tools, please visit our `code repository`_. - -If you would like to give us feedback or you run into any trouble, please send an email to artbio.ibps@gmail.com - -This tool wrapper is developed by the `ARTbio team`_ at the `Institut de Biologie Paris Seine (IBPS)`_. +For more information on the tools, or giving us feedback, please visit our `code repository`_. .. _code repository: https://github.com/ARTbio/tools-artbio/tree/master/tools/ .. _ARTbio team: http://artbio.fr -.. _Institut de Biologie Paris Seine (IBPS): http://www.ibps.upmc.fr/en/core-facilities/bioinformatics </help>