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comparison kofamscan.xml @ 4:2eb7932e91a3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 431ba943dcd0a584a64f28924396f3508c84f6b9
author iuc
date Thu, 25 Apr 2024 20:57:51 +0000
parents c3c46f14c7a4
children 8ec7636fa875
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equal deleted inserted replaced
3:c3c46f14c7a4 4:2eb7932e91a3
1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
2 <description>gene function annotation based on KEGG orthology and HMM</description> 2 <description>gene function annotation based on KEGG orthology and HMM</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.3.0</token> 4 <token name="@TOOL_VERSION@">1.3.0</token>
5 <token name="@VERSION_SUFFIX@">2</token> 5 <token name="@VERSION_SUFFIX@">3</token>
6 <xml name="reportannotation" token_selected=""> 6 <xml name="reportannotation" token_selected="">
7 <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/> 7 <param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
8 </xml> 8 </xml>
9 </macros> 9 </macros>
10 <xrefs> 10 <xrefs>
93 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/> 93 <param argument="-E" type="float" min="0.0" max="1.0" value="0.01" label="Set E-value threshold"/>
94 <section name="ap" title="Advanced parameters" expanded="true"> 94 <section name="ap" title="Advanced parameters" expanded="true">
95 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/> 95 <param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/>
96 <conditional name="f_cond"> 96 <conditional name="f_cond">
97 <param name="f_sel" type="select" label="Select output format"> 97 <param name="f_sel" type="select" label="Select output format">
98 <option value="detail" selected="true">Details for each hit (including hits below threshold) (detail)</option> 98 <option value="detail">Details for each hit (including hits below threshold) (detail)</option>
99 <option value="detail-tsv">Tab separeted values for detail format (detail-tsv)</option> 99 <option value="detail-tsv" selected="true">Tab separeted values for detail format (detail-tsv)</option>
100 <option value="mapper">KEGG Mapper compatible format (mapper)</option> 100 <option value="mapper">KEGG Mapper compatible format (mapper)</option>
101 <option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option> 101 <option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option>
102 </param> 102 </param>
103 <when value="detail"> 103 <when value="detail">
104 <expand macro="reportannotation" selected="false"/> 104 <expand macro="reportannotation" selected="false"/>