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comparison ete_lineage_generator.xml @ 11:2db72467da51 draft

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"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 67e136d433c0d925db362342919305b46fdffecd"
author earlhaminst
date Thu, 10 Mar 2022 14:01:44 +0000
parents f1eca1158f21
children d40b9a7debe5
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10:541a2ffc01ff 11:2db72467da51
1 <tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@"> 1 <tool id="ete_lineage_generator" name="ETE lineage generator" version="@VERSION@+galaxy1">
2 <description>from a list of species/taxids using the ETE Toolkit</description> 2 <description>from a list of species/taxids using the ETE Toolkit</description>
3 <macros> 3 <macros>
4 <import>ete_macros.xml</import> 4 <import>ete_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
118 <param name="speciesFile" ftype="txt" value="species.txt" /> 118 <param name="speciesFile" ftype="txt" value="species.txt" />
119 <param name="database" ftype="sqlite" value="taxdump.sqlite" /> 119 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
120 <param name="includeid" value="--includeid" /> 120 <param name="includeid" value="--includeid" />
121 <output name="outputFile" file="lineage-wid.txt" /> 121 <output name="outputFile" file="lineage-wid.txt" />
122 </test> 122 </test>
123 <test>
124 <param name="speciesFile" ftype="txt" value="species_ids.txt" />
125 <param name="database" ftype="sqlite" value="taxdump.sqlite" />
126 <output name="outputFile">
127 <assert_contents>
128 <has_line line="9606&#009;Eukaryota&#009;Chordata&#009;Mammalia&#009;Euarchontoglires&#009;Hominoidea&#009;Homo&#009;Homo sapiens"/>
129 <has_line line="0&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA&#009;NA"/>
130 </assert_contents>
131 </output>
132 <assert_stderr>
133 <has_line line="[0] could not determine lineage!"/>
134 </assert_stderr>
135 </test>
123 </tests> 136 </tests>
124 <help><![CDATA[ 137 <help><![CDATA[
125 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_. 138 Generates a table with lineage information for a list of species (also taxids and arbitrary taxons are accepted) using the `ETE Toolkit`_.
126 139
127 .. _ETE Toolkit: http://etetoolkit.org/ 140 .. _ETE Toolkit: http://etetoolkit.org/