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comparison kofamscan.xml @ 5:8ec7636fa875 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 1e2ca1537bd6d141a3494d6bb0a2f050082f7257
author iuc
date Mon, 06 May 2024 18:37:31 +0000
parents 2eb7932e91a3
children
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4:2eb7932e91a3 5:8ec7636fa875
1 <tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01"> 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@">3</token> 5 <token name="@VERSION_SUFFIX@">4</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>
65 <option value="cached" selected="true">Cached</option> 65 <option value="cached" selected="true">Cached</option>
66 <option value="compressed">Compressed set of HMM and HAL file(s)</option> 66 <option value="compressed">Compressed set of HMM and HAL file(s)</option>
67 <option value="hmm">HMM file(s)</option> 67 <option value="hmm">HMM file(s)</option>
68 </param> 68 </param>
69 <when value="cached"> 69 <when value="cached">
70 <param name="kofam" type="select"> 70 <param name="kofam" type="select" label="Kofam database to use">
71 <options from_data_table="kofam"/> 71 <options from_data_table="kofam"/>
72 <validator type="no_options" message="No option available for this input."/>
72 </param> 73 </param>
73 <param name="kofam_subset" type="select" optional="true"> 74 <param name="kofam_subset" type="select" optional="true" label="Use only a subset of the selected Kofam database" help="If nothing is selected the complete database is used">
74 <options from_data_table="kofam_subset"> 75 <options from_data_table="kofam_subset">
75 <filter type="param_value" column="2" ref="kofam"/> 76 <filter type="param_value" column="2" ref="kofam"/>
76 <filter type="sort_by" column="1"/> 77 <filter type="sort_by" column="1"/>
77 <filter type="unique_value" column="1"/> 78 <filter type="unique_value" column="1"/>
78 <column name="name" index="1"/> 79 <column name="name" index="1"/>
79 <column name="value" index="0"/> 80 <column name="value" index="0"/>
80 </options> 81 </options>
81 <validator type="no_options" message="No option available for this input"/>
82 </param> 82 </param>
83 </when> 83 </when>
84 <when value="compressed"> 84 <when value="compressed">
85 <param argument="-p" type="data" format="tar" label="Select a compressed file with HMM and HAL file(s)" help="Compressed archives are available from KofamKOALA web service (https://www.genome.jp/tools/kofamkoala/)."/> 85 <param argument="-p" type="data" format="tar" label="Select a compressed file with HMM and HAL file(s)" help="Compressed archives are available from KofamKOALA web service (https://www.genome.jp/tools/kofamkoala/)."/>
86 <param argument="-k" type="data" format="tabular" label="Select KO list file"/> 86 <param argument="-k" type="data" format="tabular" label="Select KO list file"/>