Mercurial > repos > nml > bamclipper
changeset 0:43437bfaee7d draft default tip
"planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
| author | nml |
|---|---|
| date | Tue, 28 Apr 2020 12:41:11 -0400 |
| parents | |
| children | |
| files | bamclipper.xml macros.xml test-data/SRR2075598.bam test-data/SRR2075598.primerclipped.bam test-data/trusight_myeloid.bedpe |
| diffstat | 5 files changed, 669 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamclipper.xml Tue Apr 28 12:41:11 2020 -0400 @@ -0,0 +1,87 @@ +<tool id="bamclipper" name="BAMClipper" version="@VERSION@+galaxy0"> + <description> Remove gene-specific primer sequences from BAM alignments of PCR amplicons by soft-clipping with BEDPE file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +#import re + +#set bamname = re.sub('[^\s\w-]', '_', str($input1.name)) +ln -sf '$input1' '$bamname' && +ln -sf '${input1.metadata.bam_index}' '${bamname}.bai' && + +bamclipper.sh -b '$bamname' -p '$primer_pairs' -n "\${GALAXY_SLOTS:-1}" + #if $optional.upstream: + -u '$optional.upstream' + #end if + #if $optional.downstream: + -d '$optional.downstream' + #end if + + ]]></command> + <inputs> + <param name="input1" type="data" format="bam" + label="Input Bam file" + argument="-b" + /> + <param name="primer_pairs" type="data" format="bedpe, interval" + label="BEDPE file of primer pair locations" + argument="-p" + /> + <section name="optional" title="Optional Parameters" expanded="false" > + <param name="upstream" type="integer" optional="true" + label="Upstream" + argument="-u" + help="Number of nucleotides upstream of the 5' most nucleotide of the primer (in addition to 5' most nucleotide of primer) for assigning + alignments to primers based on the alignment starting position. Default 1" + /> + <param name="downstream" type="integer" optional="true" + label="Downstream" + argument="-d" + help="Number of nucleotides downstream to the 5' most nucleotide of primer (in addition to 5' most nucleotide of primer) for assigning + alignments to primers based on the alignment starting position. Default 5" + /> + </section> + </inputs> + <outputs> + <data format_source="input1" from_work_dir="*.primerclipped.bam" name="output" label="${input1.name}.primerclipped" /> + </outputs> + <tests> + <test> + <param name="input1" value="SRR2075598.bam" /> + <param name="primer_pairs" value="trusight_myeloid.bedpe" /> + <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" /> + </test> + <test> + <param name="input1" value="SRR2075598.bam" /> + <param name="primer_pairs" value="trusight_myeloid.bedpe" /> + <section name="optional"> + <param name="upstream" value="1" /> + <param name="downstream" value="5" /> + </section> + <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" /> + </test> + </tests> + <help><![CDATA[ + +Bamclipper +---------- + +Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format +to produce a new bam file called NAME.primerclipped.bam and its associated bam index (NAME.primerclipped.bam.bai) + +Example primer pair BEDPE file lines: + +:: + + chr1 115256390 115256417 chr1 115256622 115256650 + chr1 115258642 115258664 chr1 115258876 115258903 + chr10 89692737 89692767 chr10 89692971 89692998 + chr10 89692943 89692970 chr10 89693177 89693206 + chr10 89717567 89717596 chr10 89717775 89717802 + + + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Apr 28 12:41:11 2020 -0400 @@ -0,0 +1,14 @@ +<macros> + <token name="@VERSION@">1.0.0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bamclipper</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41598-017-01703-6</citation> + <citation type="doi">10.5281/zenodo.1146014</citation> + </citations> + </xml> +</macros> \ No newline at end of file
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