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annotate virAnnot_rps2tsv.xml @ 2:0028d42d75ec draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
author iuc
date Tue, 13 May 2025 11:51:26 +0000
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0028d42d75ec planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
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1 <tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="@TOOL_VERSION@+galaxy0" profile="21.05">
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2 <description>Convert xml rpstblast results to tab file with taxonomic informations</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive"><![CDATA[
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9 python '$__tool_directory__/rps2tsv.py'
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10 -x '$rps_xml'
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11 -e '$max_evalue'
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12 -o '$output'
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13 ]]></command>
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14 <inputs>
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15 <param type="data" name="rps_xml" format="xml" label="RPSTBlast results file" />
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16 <param type="select" name="max_evalue" label="Maximum evalue">
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17 <option value="0">0</option>
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18 <option value="0.1">0.1</option>
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19 <option value="0.01">0.01</option>
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20 <option value="0.001" selected="true">0.001</option>
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21 <option value="0.0001">0.0001</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="tabular" from_work_dir="rps_result.tab" />
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="rps_xml" value="rps_test.xml"/>
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30 <param name="max_evalue" value="0.0001"/>
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31 <output name="output" file="rps_test.tab">
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32 <assert_contents>
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33 <has_n_columns n="11" />
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34 <has_n_lines n="5" />
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35 <has_text text="pfam00680, RdRP_1" />
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36 </assert_contents>
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37 </output>
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38 </test>
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39 </tests>
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40 <help><![CDATA[
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41
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42 This module takes as input rps XML file from rps motives annotation.
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43 The standard maximum evalue is 0.0001 [default value].
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44 The expected result is a tabular file. See example:
2
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45 #query_id query_length cdd_id hit_id evalue startQ endQ frame description superkingdom pident
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46 ds2020-267_4 2297 pfam00680 gnl|CDD|279070 3.12197e-05 995 1873 -2 pfam00680, RdRP_1, RNA dependent RNA polymerase. Viruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1) 16.986
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47 ds2020-267_5 2029 pfam00680 gnl|CDD|279070 8.86955e-06 840 1706 3 pfam00680, RdRP_1, RNA dependent RNA polymerase. Viruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1) 17.974
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48 ds2020-267_6 1860 pfam02123 gnl|CDD|280316 1.27376e-17 1147 1764 -1 pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Viruses(1);Riboviria(1);Orthornavirae(1);Resentoviricetes(1) 23.671
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49
0
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50
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51 ]]></help>
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52 <expand macro="citations" />
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53 </tool>