| Previous changeset 4:037f0acc7830 (2024-08-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 3efdc8b41f4f54d034d43b833733324153771fcf |
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modified:
pear.xml |
| b |
| diff -r 037f0acc7830 -r f69501361cec pear.xml --- a/pear.xml Mon Aug 12 07:15:00 2024 +0000 +++ b/pear.xml Mon Sep 02 07:41:11 2024 +0000 |
| b |
| @@ -2,7 +2,7 @@ <description>Paired-End read merger</description> <macros> <token name="@TOOL_VERSION@">0.9.6</token> - <token name="@VERSION_SUFFIX@">3</token> + <token name="@VERSION_SUFFIX@">4</token> <xml name="format_action"> <actions> <conditional name="library.type"> @@ -59,10 +59,10 @@ --quality-theshold $quality_threshold --max-uncalled-base $max_uncalled_base --test-method $test_method - --empirical-freqs $empirical_freqs --threads "\${GALAXY_SLOTS:-8}" --score-method $score_method --cap $cap + $empirical_freqs $nbase ]]> </command> @@ -93,7 +93,7 @@ <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option> <option value="2">Use the acceptance probability (2)</option> </param> - <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/> + <param name="empirical_freqs" type="boolean" truevalue="--empirical-freqs" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/> <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" label="Use N base if uncertain" help="When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)"/> <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> <option value="1">OES with +1 for match and -1 for mismatch</option> |