Mercurial > repos > iuc > ivar_consensus
changeset 14:e4ee04da1c19 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
| author | iuc |
|---|---|
| date | Sat, 25 Mar 2023 12:53:47 +0000 |
| parents | 1069f6db0a0e |
| children | ede363a64152 |
| files | ivar_consensus.xml macros.xml |
| diffstat | 2 files changed, 3 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/ivar_consensus.xml Mon Feb 13 17:30:23 2023 +0000 +++ b/ivar_consensus.xml Sat Mar 25 12:53:47 2023 +0000 @@ -21,8 +21,6 @@ ]]></command> <inputs> <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> - <!-- Warning: integer params in the following define a max of 255 intentionally - because the underlying C++ code of ivar defines them as uint8 and does not check for overflow! --> <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/> <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.0" label="Minimum frequency threshold"> <help> @@ -36,7 +34,7 @@ </help> </param> <param name="min_indel_freq" argument="-c" type="float" min="0" max="1" value="0.8" label="Minimum indel frequency threshold" help="Same meaning as the "Minimum frequency threshold" above, but applied to indels."/> - <param name="min_depth" argument="-m" type="integer" min="1" max="255" value="10" label="Minimum depth to call consensus"/> + <param name="min_depth" argument="-m" type="integer" min="1" value="10" label="Minimum depth to call consensus"/> <param name="depth_action" type="select" label="How to represent positions with coverage less than the minimum depth threshold"> <option value="-k">Drop from output (-k)</option> <option value="-n N" selected="true">Represent as N (-n N)</option>
--- a/macros.xml Mon Feb 13 17:30:23 2023 +0000 +++ b/macros.xml Sat Mar 25 12:53:47 2023 +0000 @@ -1,11 +1,11 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.3.2</token> + <token name="@TOOL_VERSION@">1.4.0</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">ivar</requirement> - <requirement type="package" version="3.10.8">python</requirement> + <requirement type="package" version="3.11.0">python</requirement> <requirement type="package" version="1.16.1">samtools</requirement> <yield/> </requirements>