Mercurial > repos > artbio > pindel
diff 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 |
parents | |
children | 078c6ab38858 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pindelwrapper.xml Wed Sep 29 21:30:31 2021 +0000 @@ -0,0 +1,101 @@ +<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>