Mercurial > repos > iuc > virannot_rps2tsv
diff virAnnot_rps2tsv.xml @ 0:bbaa89f070f4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
author | iuc |
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date | Mon, 04 Mar 2024 19:56:16 +0000 |
parents | |
children | 84d20d9c292d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/virAnnot_rps2tsv.xml Mon Mar 04 19:56:16 2024 +0000 @@ -0,0 +1,57 @@ +<tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="1.0.0+galaxy0" profile="21.05"> + <description>Convert xml rpstblast results to tab file with taxonomic informations</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/rps2tsv.py' + -x '$rps_xml' + -e '$max_evalue' + -o '$output' + ]]></command> + <inputs> + <param type="data" name="rps_xml" format="xml" label="RPSTBlast results file" /> + <param type="select" name="max_evalue" label="Maximum evalue"> + <option value="0">0</option> + <option value="0.1">0.1</option> + <option value="0.01">0.01</option> + <option value="0.001" selected="true">0.001</option> + <option value="0.0001">0.0001</option> + </param> + </inputs> + <outputs> + <data name="output" format="tabular" from_work_dir="rps_result.tab" /> + </outputs> + <tests> + <test> + <param name="rps_xml" value="rps_test.xml"/> + <param name="max_evalue" value="0.0001"/> + <output name="output" file="rps_test.tab"> + <assert_contents> + <has_n_columns n="10" /> + <has_n_lines n="105" /> + </assert_contents> + </output> + </test> + <test> + <param name="rps_xml" value="rps_test.xml"/> + <param name="max_evalue" value="0.0001"/> + <output name="output" file="rps_test.tab"> + <assert_contents> + <has_text text="pfam01333, Apocytochr_F_C, Apocytochrome F" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +This module takes as input rps XML file from rps motives annotation. +The standard maximum evalue is 0.0001 [default value]. +The expected result is a tabular file. See example: +#query_id query_length cdd_id hit_id evalue startQ endQ frame description superkingdom +ds2020-267_120 339 pfam01333 gnl|CDD|366578 0.000848733 197 325 -3 pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034. Eukaryota(227);Bacteria(73); + + ]]></help> + <expand macro="citations" /> +</tool>