Mercurial > repos > ebi-gxa > fastq_trim_poly_at
view fastq_trim_poly_at.xml @ 1:ebca4912eabe draft default tip
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 94b7fe8e2147adc32748e2921729b99669e13a1b"
author | ebi-gxa |
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date | Tue, 15 Feb 2022 16:38:32 +0000 |
parents | dcc82e999439 |
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<tool id="fastq_trim_poly_at" name="FASTQ poly-A|T trimmer" profile="18.01" version="0.25.1+galaxy0"> <description>Trims poly-A stretches at the 3'-end and poly-T at 5'-end of each read, optionally discarding reads with a length below the given threshold.</description> <requirements> <requirement type="package" version="0.25.1">fastq_utils</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ fastq_trim_poly_at --file '$file' --outfile '$outfile' #if '$min_poly_at_len': --min_poly_at_len '$min_poly_at_len' #end if #if '$min_len': --min_len '$min_len' #end if ]]></command> <inputs> <param name="file" label="Input file" argument="--file" type="data" format="fastqsanger.gz" optional="false" help="Fastq (optional gzipped) file name"/> <param name="min_poly_at_len" label="Minimum Poly-AT Length" argument="--min_poly_at_len" optional="true" type="integer" min="0" help="Minimum length of poly-A|T sequence to remove"/> <param name="min_len" label="Minimum Quality" optional="true" value="" argument="--min_qual" type="integer" help="Minimum read length"/> </inputs> <outputs> <data label="${tool.name} on ${on_string}: Output file" name="outfile" format="fastqsanger.gz" /> </outputs> <tests> <test> <param name="file" value="poly_at.fastq.gz"/> <param name="min_poly_at_len" value="3"/> <output name="outfile" file="poly_at_len3.fastq.gz" compare="sim_size" delta_frac="0.1"/> </test> </tests> <help><![CDATA[ ======================================================= FASTQ poly-A|T trimmer (fastq_trim_poly_at) ======================================================= Minimum Poly-AT Length - The terminal poly-A|T sequence should be at least this long to be removed Minimum Length - Reads with post-trimming length less than this setting will be removed ]]></help> <citations> <citation type="bibtex"><![CDATA[ @ARTICLE{Fonseca2017, author = {Fonseca, N.}, title = {fastq_utils}, year = {2017}, publisher = {GitHub}, journal = {GitHub repository}, howpublished = {\url{https://github.com/nunofonseca/fastq_utils}}, commit = {c6cf3f954c5286e62fbe36bb9ffecd89d7823b07} }]]></citation> </citations> </tool>