Mercurial > repos > iuc > ivar_trim
changeset 13:f0cc9cf99407 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit a16957b7f6cb8687daafb005c0036abebce59b26
| author | iuc |
|---|---|
| date | Fri, 10 Feb 2023 17:32:03 +0000 |
| parents | e3bb03cf207a |
| children | bcaa0d571ce2 |
| files | ivar_trim.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/ivar_trim.xml Wed Jan 11 09:55:20 2023 +0000 +++ b/ivar_trim.xml Fri Feb 10 17:32:03 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy5" profile="@PROFILE@"> +<tool id="ivar_trim" name="ivar trim" version="@TOOL_VERSION@+galaxy6" profile="@PROFILE@"> <description>Trim reads in aligned BAM</description> <macros> <import>macros.xml</import> @@ -26,7 +26,7 @@ ivar trim -i sorted.bam -b bed.bed - #if $amplicons.filter_by == 'yes' + #if $amplicons.filter_by == 'yes' or $amplicons.filter_by == 'yes_compute' -f amplicon_info.tsv #end if -x $primer_pos_wiggle @@ -75,8 +75,8 @@ help="Reads that occur at the specified offset positions relative to primer positions (as annotated in the primer information dataset) will also be trimmed (default: 0)" /> <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads not ending in any primer binding sites?"/> <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/> - <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/> - <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/> + <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality threshold for sliding window to pass"/> + <param name="window_width" argument="-s" type="integer" min="0" max="255" value="4" label="Width of sliding window"/> </inputs> <outputs> <data name="output_bam" format="bam" label="${tool.name} on ${on_string} Trimmed bam" from_work_dir="trimmed.sorted.bam"/>