Mercurial > repos > iuc > virannot_rps2tsv

annotate virAnnot_rps2tsv.xml @ 5:aac02a3a395c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 31e7eb490fbaa2b1f34f0e0f154a6f82ad2f2f82
author iuc
date Mon, 04 Aug 2025 19:14:00 +0000
parents 998724a43694
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
aac02a3a395c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 31e7eb490fbaa2b1f34f0e0f154a6f82ad2f2f82
iuc
parents: 4
diff changeset
1 <tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
0
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
2 <description>Convert xml rpstblast results to tab file with taxonomic informations</description>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
3 <macros>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
4 <import>macros.xml</import>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
5 </macros>
1
84d20d9c292d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 48a3a1fa033745898a131f9dca7132947683c02f
iuc
parents: 0
diff changeset
6 <expand macro="xrefs"/>
0
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
7 <expand macro="requirements" />
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
8 <command detect_errors="aggressive"><![CDATA[
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
9 python '$__tool_directory__/rps2tsv.py'
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
10 -x '$rps_xml'
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
11 -e '$max_evalue'
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
12 -o '$output'
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
13 ]]></command>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
14 <inputs>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
15 <param type="data" name="rps_xml" format="xml" label="RPSTBlast results file" />
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
16 <param type="select" name="max_evalue" label="Maximum evalue">
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
17 <option value="0">0</option>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
18 <option value="0.1">0.1</option>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
19 <option value="0.01">0.01</option>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
20 <option value="0.001" selected="true">0.001</option>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
21 <option value="0.0001">0.0001</option>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
22 </param>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
23 </inputs>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
24 <outputs>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
25 <data name="output" format="tabular" from_work_dir="rps_result.tab" />
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
26 </outputs>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
27 <tests>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
28 <test>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
29 <param name="rps_xml" value="rps_test.xml"/>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
30 <param name="max_evalue" value="0.0001"/>
5
aac02a3a395c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 31e7eb490fbaa2b1f34f0e0f154a6f82ad2f2f82
iuc
parents: 4
diff changeset
31 <output name="output">
0
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
32 <assert_contents>
4
998724a43694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
33 <has_n_columns n="11" />
3
d1fd5579469d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 2
diff changeset
34 <has_n_lines n="5" />
2
fd7104249a3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 1
diff changeset
35 <has_text text="pfam00680, RdRP_1" />
0
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
36 </assert_contents>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
37 </output>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
38 </test>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
39 </tests>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
40 <help><![CDATA[
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
41
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
42 This module takes as input rps XML file from rps motives annotation.
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
43 The standard maximum evalue is 0.0001 [default value].
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
44 The expected result is a tabular file. See example:
4
998724a43694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
45 #query_id query_length cdd_id hit_id evalue startQ endQ frame description superkingdom pident
998724a43694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
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
998724a43694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
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
998724a43694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
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
998724a43694 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
49
0
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
50
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
51 ]]></help>
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
52 <expand macro="citations" />
bbaa89f070f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
53 </tool>