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Merge pull request #1486 from davebx/flash
Wrap FLASH version 1.2.11
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| categories: | ||
| - Assembly | ||
| - Fastq Manipulation | ||
| description: Fast Length Adjustment of SHort reads | ||
| homepage_url: https://ccb.jhu.edu/software/FLASH/ | ||
| long_description: | | ||
| FLASH is an accurate and fast tool to merge paired-end reads that were | ||
| generated from DNA fragments whose lengths are shorter than twice the | ||
| length of reads. | ||
| name: flash | ||
| owner: iuc | ||
| remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash | ||
| type: unrestricted |
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| <?xml version="1.0"?> | ||
| <tool id="flash" name="FLASH" version="1.2.11"> | ||
| <description>adjust length of short reads</description> | ||
| <requirements> | ||
| <requirement type="package" version="1.2.11">flash</requirement> | ||
| </requirements> | ||
| <version_command>flash --version | head -n 1</version_command> | ||
| <command detect_errors="aggressive"> | ||
| <![CDATA[ | ||
| flash --threads=\${GALAXY_SLOTS:-1} | ||
| -m $min_overlap | ||
| -M $max_overlap | ||
| -x $max_mismatch_density | ||
| $allow_outies | ||
| '$forward' '$reverse' | ||
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param format="fastq" name="forward" type="data" label="Forward reads" /> | ||
| <param format="fastq" name="reverse" type="data" label="Reverse reads" /> | ||
| <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." /> | ||
| <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." /> | ||
| <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." /> | ||
| <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." /> | ||
| </inputs> | ||
| <outputs> | ||
| <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" /> | ||
| <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" /> | ||
| <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" /> | ||
| <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" /> | ||
| <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram" /> | ||
| <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" > | ||
| <filter>allow_outies</filter> | ||
| </data> | ||
| <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" > | ||
| <filter>allow_outies</filter> | ||
| </data> | ||
| <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" > | ||
| <filter>allow_outies</filter> | ||
| </data> | ||
| <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" > | ||
| <filter>allow_outies</filter> | ||
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <param name="forward" value="flash_forward_in1.fastq" /> | ||
| <param name="reverse" value="flash_reverse_in1.fastq" /> | ||
| <output name="merged_reads" file="flash_merged_out1.fastq" /> | ||
| <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" /> | ||
| <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" /> | ||
| <output name="hist" file="flash_hist_out1.tabular" /> | ||
| <output name="histogram" file="flash_hist_out1.txt" /> | ||
| </test> | ||
| <test> | ||
| <param name="forward" value="flash_forward_in2.fastq" /> | ||
| <param name="reverse" value="flash_reverse_in2.fastq" /> | ||
| <param name="allow_outies" value="true" /> | ||
| <output name="merged_reads" file="flash_merged_out2.fastq" /> | ||
| <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" /> | ||
| <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" /> | ||
| <output name="hist" file="flash_hist_out2.tabular" /> | ||
| <output name="histogram" file="flash_hist_out2.txt" /> | ||
| <output name="hist_in" file="flash_hist_in_out2.tabular" /> | ||
| <output name="histogram_in" file="flash_hist_in_out2.txt" /> | ||
| <output name="hist_out" file="flash_hist_out_out2.tabular" /> | ||
| <output name="histogram_out" file="flash_hist_out_out2.txt" /> | ||
| </test> | ||
| </tests> | ||
| <help> | ||
| <![CDATA[ | ||
| FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool | ||
| to merge paired-end reads that were generated from DNA fragments whose | ||
| lengths are shorter than twice the length of reads. Merged read pairs result | ||
| in unpaired longer reads, which are generally more desired in genome | ||
| assembly and genome analysis processes. | ||
| Briefly, the FLASH algorithm considers all possible overlaps at or above a | ||
| minimum length between the reads in a pair and chooses the overlap that | ||
| results in the lowest mismatch density (proportion of mismatched bases in | ||
| the overlapped region). Ties between multiple overlaps are broken by | ||
| considering quality scores at mismatch sites. When building the merged | ||
| sequence, FLASH computes a consensus sequence in the overlapped region. | ||
| ]]> | ||
| </help> | ||
| <citations> | ||
| <citation type="doi">10.1093/bioinformatics/btr507</citation> | ||
| </citations> | ||
| </tool> |
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