Mercurial > repos > artbio > pindel
view pindelwrapper.xml @ 0:decc6b5631dc draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
author | artbio |
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date | Wed, 29 Sep 2021 21:30:31 +0000 |
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children | 078c6ab38858 |
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<tool id ="pindel" name="Pindel" version="0.2.5b8+galaxy1"> <description></description> <requirements> <requirement type="package" version="0.2.5b8">pindel</requirement> <requirement type="package" version="1.0">openssl</requirement> <requirement type="package" version="1.7">samtools</requirement> <requirement type="package" version="3.7">python</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ ln -f -s "$input_file.metadata.bam_index" alignment.sorted.bam.bai && ln -f -s "$input_file" alignment.sorted.bam && ln -f -s "$reference" ref.fa && samtools faidx ref.fa && python $__tool_directory__/create_config_file.py --input_file alignment.sorted.bam --insert_size "$insert_size" --sample_label "$input_file.element_identifier" --output_config_file output_config_file && pindel -f ref.fa -i output_config_file -c "$chromosome" -o prefix && mv prefix_D $Deletions && mv prefix_SI $Short_Insertions && mv prefix_LI $Long_Insertions && mv prefix_INV $Inversions && mv prefix_TD $Tandem_Duplications && mv prefix_RP $Read_Pair && mv prefix_INT_final $int_final && mv prefix_CloseEndMapped $Close_End_Mapped ]]></command> <inputs> <param format="bam" name="input_file" type="data" label="One or more BAM alignment files produced by BWA"/> <param name="insert_size" type="integer" value="" label="Expected Insert size" /> <param format="fasta" name="reference" type="data" label="Reference genome in fasta format"/> <param name="chromosome" type="text" value="ALL" help="Select a chromsome. ALL will use all chromosomes" label="Which chromosome to operate on"/> </inputs> <outputs> <data format="txt" name="Deletions" label="${input_file.element_identifier} Deletions"/> <data format="txt" name="Short_Insertions" label="${input_file.element_identifier} Short Insertions"/> <data format="txt" name="Long_Insertions" label="${input_file.element_identifier} Long Insertions"/> <data format="txt" name="Inversions" label="${input_file.element_identifier} Inversions"/> <data format="txt" name="Tandem_Duplications" label="${input_file.element_identifier} Tandem Duplications"/> <data format="txt" name="Breakpoints" label="${input_file.element_identifier} Breakpoints"/> <data format="txt" name="Read_Pair" label="${input_file.element_identifier} Read Pair Evidence"/> <data format="txt" name="int_final" label="${input_file.element_identifier} INT_final"/> <data format="txt" name="Close_End_Mapped" label="${input_file.element_identifier} Close End Mapped"/> </outputs> <tests> <test> <param name="input_file" value="X_100000_Hum1.bam" ftype="bam"/> <param name="insert_size" value="250"/> <param name="reference" value="dm6_X.fasta" ftype="fasta"/> <param name="chromosome" value="ALL"/> <output name="Deletions" file="X_100000_Hum1.bam_Deletions.txt" ftype="txt"/> <output name="Short_Insertions" file="X_100000_Hum1.bam_Short_Insertions.txt" ftype="txt"/> <output name="Long_Insertions" file="X_100000_Hum1.bam_Long_Insertions.txt" ftype="txt"/> <output name="Inversions" file="X_100000_Hum1.bam_Inversions.txt" ftype="txt"/> <output name="Tandem_Duplications" file="X_100000_Hum1.bam_Tandem_Duplications.txt" ftype="txt"/> <output name="Breakpoints" file="X_100000_Hum1.bam_Breakpoints.txt" ftype="txt"/> <output name="Read_Pair" file="X_100000_Hum1.bam_Read_Pair_Evidence.txt" ftype="txt"/> <output name="int_final" file="X_100000_Hum1.bam_INT_final.txt" ftype="txt"/> <output name="Close_End_Mapped" file="X_100000_Hum1.bam_Close_End_Mapped.txt" ftype="txt"/> </test> </tests> <help> <![CDATA[ Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequencing data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. The following inputs/parameters are required: - One or more BAM alignment files produced by BWA - Expected Insert Size for each alignment file - Sample label for each alignment file - Reference genome in fasta format (the same one used in alignment) - Which chromosome to operate on The following output files are produced by Pindel: - Deletions - Short Insertions - Long Insertions - Inversions - Tandom Duplications - Breakpoints - Read Pair Evidence - INT_final - Close End Mapped ]]> </help> <citations> <citation type="doi">doi:10.1093/bioinformatics/btp394</citation> </citations> </tool>