Mercurial > repos > ebi-gxa > fastq_trim_poly_at
diff fastq_trim_poly_at.xml @ 0:dcc82e999439 draft
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils commit 3922947623a7f343e3d0475e82b72bba75c794e7"
author | ebi-gxa |
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date | Tue, 15 Feb 2022 07:54:15 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq_trim_poly_at.xml Tue Feb 15 07:54:15 2022 +0000 @@ -0,0 +1,56 @@ +<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>