Mercurial > repos > iuc > filtlong
changeset 6:0d9cd7b02f14 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong commit 5875d08292df3ceac45962dcc1790a36de9dcf9a
| author | iuc |
|---|---|
| date | Tue, 23 Sep 2025 16:33:10 +0000 |
| parents | 1dfbdcbf604b |
| children | |
| files | filtlong.xml macros.xml |
| diffstat | 2 files changed, 32 insertions(+), 24 deletions(-) [+] |
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--- a/filtlong.xml Mon Aug 18 12:38:23 2025 +0000 +++ b/filtlong.xml Tue Sep 23 16:33:10 2025 +0000 @@ -50,10 +50,16 @@ <inputs> <param name="input_file" type="data" format="fastqsanger,fastqsanger.gz" label="Input FASTQ" help="FASTQ of input reads"/> <section name="output_thresholds" title="Output thresholds"> - <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/> + <param argument="--target_bases" type="text" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases (unit suffixes: k, kb, m, mb, g, gb)."> + <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator> + </param> <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/> - <param argument="--max_length" type="integer" min="0" optional="True" label="Max. length" help="Maximum length threshold"/> - <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/> + <param argument="--max_length" type="text" min="0" optional="True" label="Max. length" help="Maximum length threshold (unit suffixes: k, kb, m, mb, g, gb)"> + <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator> + </param> + <param argument="--min_length" type="text" min="0" optional="True" label="Min. length" help="Minimum length threshold (unit suffixes: k, kb, m, mb, g, gb)"> + <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator> + </param> <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/> <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/> </section> @@ -69,7 +75,9 @@ </section> <section name="read_manipulation" title="Read manipulation"> <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/> - <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/> + <param argument="--split" type="text" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"> + <validator type="regex" message="Invalid characters in field">(?i)^[0-9]+(?:[KMG](?:B)?)?$</validator> + </param> </section> <section name="other" title="Other"> <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/> @@ -84,7 +92,7 @@ <section name="output_thresholds"> <param name="min_length" value="1000"/> <param name="keep_percent" value="50"/> - <param name="target_bases" value="500000000"/> + <param name="target_bases" value="500mb"/> </section> <output name="outfile" ftype="fastqsanger" file="output.fastq"/> </test> @@ -98,7 +106,7 @@ <section name="output_thresholds"> <param name="min_length" value="1000"/> <param name="keep_percent" value="90"/> - <param name="target_bases" value="500000000"/> + <param name="target_bases" value="500mb"/> </section> <section name="read_manipulation"> <param name="trim" value="True"/> @@ -117,16 +125,5 @@ <help><![CDATA[ Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. ]]></help> - <citations> - <citation type="bibtex"> - @misc{rrwick2017, - author = {Wick, Ryan}, - year = {2017}, - title = {Filtlong}, - publisher = {GitHub}, - journal = {GitHub repository}, - url = {https://github.com/rrwick/Filtlong}, - } - </citation> - </citations> + <expand macro="citations"/> </tool>
--- a/macros.xml Mon Aug 18 12:38:23 2025 +0000 +++ b/macros.xml Tue Sep 23 16:33:10 2025 +0000 @@ -1,12 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">0.3.0</token> + <token name="@TOOL_VERSION@">0.3.1</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.01</token> <xml name="biotools"> <xrefs> - <xref type="bio.tools"> - filtlong - </xref> + <xref type="bio.tools">filtlong</xref> </xrefs> </xml> <xml name="requirements"> @@ -14,5 +12,18 @@ <requirement type="package" version="@TOOL_VERSION@">filtlong</requirement> </requirements> </xml> -</macros> - + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{rrwick2017, + author = {Wick, Ryan}, + year = {2017}, + title = {Filtlong}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/rrwick/Filtlong}, + } + </citation> + </citations> + </xml> +</macros> \ No newline at end of file