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comparison pear.xml @ 5:f69501361cec draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 3efdc8b41f4f54d034d43b833733324153771fcf
author iuc
date Mon, 02 Sep 2024 07:41:11 +0000
parents 037f0acc7830
children
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4:037f0acc7830 5:f69501361cec
1 <tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="23.0"> 1 <tool id="iuc_pear" name="Pear" version="@TOOL_VERSION@.@VERSION_SUFFIX@" profile="23.0">
2 <description>Paired-End read merger</description> 2 <description>Paired-End read merger</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.9.6</token> 4 <token name="@TOOL_VERSION@">0.9.6</token>
5 <token name="@VERSION_SUFFIX@">3</token> 5 <token name="@VERSION_SUFFIX@">4</token>
6 <xml name="format_action"> 6 <xml name="format_action">
7 <actions> 7 <actions>
8 <conditional name="library.type"> 8 <conditional name="library.type">
9 <when value="paired"> 9 <when value="paired">
10 <action type="format"> 10 <action type="format">
57 --min-asm-length $min_assembly_length 57 --min-asm-length $min_assembly_length
58 --min-trim-length $min_trim_length 58 --min-trim-length $min_trim_length
59 --quality-theshold $quality_threshold 59 --quality-theshold $quality_threshold
60 --max-uncalled-base $max_uncalled_base 60 --max-uncalled-base $max_uncalled_base
61 --test-method $test_method 61 --test-method $test_method
62 --empirical-freqs $empirical_freqs
63 --threads "\${GALAXY_SLOTS:-8}" 62 --threads "\${GALAXY_SLOTS:-8}"
64 --score-method $score_method 63 --score-method $score_method
65 --cap $cap 64 --cap $cap
65 $empirical_freqs
66 $nbase 66 $nbase
67 ]]> 67 ]]>
68 </command> 68 </command>
69 <inputs> 69 <inputs>
70 <conditional name="library"> 70 <conditional name="library">
91 <param argument="--cap" type="integer" value="40" min="0" label="Specify the upper bound for the resulting quality score" help="If set to zero, capping is disabled."/> 91 <param argument="--cap" type="integer" value="40" min="0" label="Specify the upper bound for the resulting quality score" help="If set to zero, capping is disabled."/>
92 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)"> 92 <param name="test_method" type="select" label="Type of statistical test" help="(--test-method)">
93 <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option> 93 <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option>
94 <option value="2">Use the acceptance probability (2)</option> 94 <option value="2">Use the acceptance probability (2)</option>
95 </param> 95 </param>
96 <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/> 96 <param name="empirical_freqs" type="boolean" truevalue="--empirical-freqs" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/>
97 <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)"/> 97 <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)"/>
98 <param name="score_method" type="select" label="Scoring method" help="(--score-method)"> 98 <param name="score_method" type="select" label="Scoring method" help="(--score-method)">
99 <option value="1">OES with +1 for match and -1 for mismatch</option> 99 <option value="1">OES with +1 for match and -1 for mismatch</option>
100 <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option> 100 <option value="2" selected="true">Assembly score (AS) use +1 for match and -1 for mismatch multiplied by base quality scores</option>
101 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option> 101 <option value="3">Ignore quality scores and use +1 for a match and -1 for a mismatch</option>