Mercurial > repos > bgruening > hifiasm
changeset 15:60024a528cbd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm commit dfa44145539a0897f369311667dbe4ca27ff7dc4
| author | bgruening |
|---|---|
| date | Fri, 13 Oct 2023 07:26:01 +0000 |
| parents | 71740308d412 |
| children | 41cea2aa2dce |
| files | hifiasm.xml |
| diffstat | 1 files changed, 17 insertions(+), 1 deletions(-) [+] |
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--- a/hifiasm.xml Wed May 10 07:05:39 2023 +0000 +++ b/hifiasm.xml Fri Oct 13 07:26:01 2023 +0000 @@ -1,7 +1,7 @@ <tool id="hifiasm" name="Hifiasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>haplotype-resolved de novo assembler for PacBio Hifi reads</description> <macros> - <token name="@TOOL_VERSION@">0.19.5</token> + <token name="@TOOL_VERSION@">0.19.7</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@FORMATS@">fasta,fasta.gz,fastq,fastq.gz</token> <xml name="reads"> @@ -115,6 +115,12 @@ --n-hap $purge_options.n_hap #end if #end if + #if str($scaffolding_options.scaffold_selector) == 'set': + --dual-scaf + #if $scaffolding_options.scaf_gap: + --scaf-gap $scaffolding_options.scaf_gap + #end if + #end if #if str($hic_partition.hic_partition_selector) == 'set': --h1 ${ ','.join(["'%s'" % $x for $x in $hic1_inputs]) } @@ -273,6 +279,16 @@ </param> </when> </conditional> + <conditional name="scaffolding_options"> + <param name="scaffold_selector" type="select" label="Options for hifiasm scaffolding"> + <option value="blank">No scaffolding (default)</option> + <option value="set">Turn on hifiasm scaffolding</option> + </param> + <when value="blank" /> + <when value="set"> + <param argument="--scaf-gap" type="integer" min="1" value="3000000" optional="true" label="Max scaffolding gap size" help="Set the max gap size of scaffolds (default is 3,000,000)" /> + </when> + </conditional> <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no" /> <param name="bins_out" type="boolean" label="Output .bin files (used for development and debugging)?" truevalue="yes" falsevalue="no" /> </inputs>