Mercurial > repos > jackcurragh > ribogalaxy_create_ribosome_profile
comparison create_ribosome_profile/create_ribosome_profile.xml @ 1:e97985309423 draft
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| author | jackcurragh |
|---|---|
| date | Wed, 20 Apr 2022 15:08:26 +0000 |
| parents | 06b01eb16c4e |
| children | f55468c622fa |
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| 0:06b01eb16c4e | 1:e97985309423 |
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| 2 <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description> | 2 <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.79">biopython</requirement> | 4 <requirement type="package" version="1.79">biopython</requirement> |
| 5 <requirement type="package" version="0.19.0">pysam</requirement> | 5 <requirement type="package" version="0.19.0">pysam</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4}</command> | 7 <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4} ${output1}</command> |
| 8 <inputs> | 8 <inputs> |
| 9 <param name="input1" type="data" format="bam" label="BAM file to process"/> | 9 <param name="input1" type="data" format="bam" label="BAM file to process"/> |
| 10 <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/> | 10 <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/> |
| 11 <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/> | 11 <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/> |
| 12 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase"> | 12 <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase"> |