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Update tools/ragtag to 2.1.1 #8908

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Merged
bernt-matthias merged 4 commits into from
Nov 13, 2026
Merged

Update tools/ragtag to 2.1.1 #8908

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79b70cc
Updating tools/ragtag from version 2.1.0 to 2.1.1
Oct 30, 2026
7225a75
Update ragtag to 2.1.1
SaimMomin12 Nov 12, 2026
96c166f
Remove whitespaces
SaimMomin12 Nov 12, 2026
f344c59
More whitespaces
SaimMomin12 Nov 12, 2026
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46 changes: 17 additions & 29 deletions tools/ragtag/macros.xml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
<macros>
<token name="@TOOL_VERSION@">2.1.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@TOOL_VERSION@">2.1.1</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">25.1</token>
<xml name="xrefs">
<xrefs>
<xref type="bio.tools">ragtag</xref>
</xrefs>
<xrefs>
<xref type="bio.tools">ragtag</xref>
</xrefs>
</xml>
<xml name="requirements">
<requirements>
Expand All @@ -18,26 +19,15 @@
</xml>
<xml name="input_options">
<param name="reference" type="data" format="fasta" label="Reference FASTA file"/>
<param name="query" type="data" format="fasta" label="Query FASTA file" />
<param name="query" type="data" format="fasta" label="Query FASTA file"/>
</xml>
<xml name="common_parameters">
<param argument="-e" type="data" format="txt" optional="true" label="List of reference headers to ignore"
help="Use this parameter to provide a single column file listing any reference.fa headers that should
be ignored (e.g. chr0/chrUn or alt contigs)"/>
<param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave uncorrected"
help="use this parameter to provide a single column file listing any query.fa headers that shall not be broken"/>
<param argument="-f" type="integer" min="0" value="1000" label="Minimum unique single length"
help="If an alignment is not entirely unique, at least -f bp of the alignment must be unique to be considered
for scaffolding. By default, entirely unique alignments are considered regardless of their length, but
this can be disabled with --remove-small. Doing so ensures that only alignments at least -f bp in length
are considered for correction"/>
<param argument="--remove-small" type="boolean" truevalue="--remove-small"
falsevalue="" checked="false" label="Remove unique alignments"
help="Remove unique alignments shorter than the minimum unique alignment length" />
<param argument="-q" type="integer" min="0" value="10" label="Minimum mappping quality"
help="Mapping quality scores quantify the probability that a read is misplaced" />
<param argument="-d" type="integer" min="0" value="100000" label="Maximum alignment merge distance"
help="For each query sequence, syntenic alignments within -d bp of each other are merged into longer alignments"/>
<param argument="-e" type="data" format="txt" optional="true" label="List of reference headers to ignore" help="Use this parameter to provide a single column file listing any reference.fa headers that should be ignored (e.g. chr0/chrUn or alt contigs)"/>
<param argument="-j" type="data" format="txt" optional="true" label="List of query headers to leave uncorrected" help="use this parameter to provide a single column file listing any query.fa headers that shall not be broken"/>
<param argument="-f" type="integer" min="0" value="1000" label="Minimum unique single length" help="If an alignment is not entirely unique, at least -f bp of the alignment must be unique to be considered for scaffolding. By default, entirely unique alignments are considered regardless of their length, but this can be disabled with --remove-small. Doing so ensures that only alignments at least -f bp in length are considered for correction"/>
<param argument="--remove-small" type="boolean" truevalue="--remove-small" falsevalue="" checked="false" label="Remove unique alignments" help="Remove unique alignments shorter than the minimum unique alignment length"/>
<param argument="-q" type="integer" min="0" value="10" label="Minimum mappping quality" help="Mapping quality scores quantify the probability that a read is misplaced"/>
<param argument="-d" type="integer" min="0" value="100000" label="Maximum alignment merge distance" help="For each query sequence, syntenic alignments within -d bp of each other are merged into longer alignments"/>
<conditional name="mapping_conditional">
<param name="mapping_option" type="select" label="Aligner tool">
<option value="nucmer">Nucmer</option>
Expand All @@ -56,12 +46,10 @@
<param argument="-c" type="integer" min="0" value="500" label="Minimum length of a cluster of matches"/>
</when>
<when value="minimap2">
<param argument="--mm2-params" type="select"
label="Select a profile of preset options"
help="Each profile comes with the preconfigured settings mentioned in parentheses" >
<option value="asm5">Asm5: the alignment will not extend to regions with 5% or higher sequence divergence (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100)</option>
<option value="asm10">Asm10: up to 10% sequence divergence (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
<option value="asm20">Asm20: up to 20% sequence divergence (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
<param argument="--mm2-params" type="select" label="Select a profile of preset options" help="Each profile comes with the preconfigured settings mentioned in parentheses">
<option value="asm5">Asm5: the alignment will not extend to regions with 5% or higher sequence divergence (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 --min-occ-floor=100)</option>
<option value="asm10">Asm10: up to 10% sequence divergence (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
<option value="asm20">Asm20: up to 20% sequence divergence (-k19 -w10 -A1 -B6 -O6,26 -E2,1 -s200 -z200 --min-occ-floor=100)</option>
</param>
</when>
</conditional>
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