Mercurial > repos > cpt > cpt_blastn_to_gff
comparison cpt_blastn_to_gff/blastn_to_gff3.xml @ 0:54c3aabcb3e7 draft
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author | cpt |
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date | Fri, 13 May 2022 04:42:45 +0000 |
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-1:000000000000 | 0:54c3aabcb3e7 |
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1 <tool id="edu.tamu.cpt.blastn_to_gff3" name="BlastN Results to GFF3" version="19.1.0.0"> | |
2 <description>converts blast xml or tabular results to a JBrowse-compatible file</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 <import>cpt-macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <command detect_errors="aggressive"><![CDATA[ | |
9 $__tool_directory__/blast_to_gff3.py | |
10 $input_type.blast_input | |
11 #if $input_type.input_type_selector == "xml": | |
12 --blastxml | |
13 #elif $input_type.input_type_selector == "tsv": | |
14 --blasttab | |
15 #end if | |
16 > $output]]></command> | |
17 <inputs> | |
18 <conditional name="input_type"> | |
19 <param name = "input_type_selector" type="select" label="Choose BlastN File Format"> | |
20 <option value="xml" selected="true">BlastXML</option> | |
21 <option value="tsv">Blast 25 Column Table"</option> | |
22 </param> | |
23 <when value="xml"> | |
24 <param name="blast_input" type="data" format="xml" label="BlastXML Input"/> | |
25 </when> | |
26 <when value="tsv"> | |
27 <param name="blast_input" type="data" format="tabular" label="Blast 25 Column Table"/> | |
28 </when> | |
29 </conditional> | |
30 </inputs> | |
31 <outputs> | |
32 <data format="gff3" name="output"/> | |
33 </outputs> | |
34 <tests> | |
35 <test> | |
36 <param name="input_type_selector" value="xml"/> | |
37 <param name="blast_input" value="BlastnXmlToGff_In.blastxml" /> | |
38 <output name="output" file="BlastnXmlToGff_Out.gff3" /> | |
39 </test> | |
40 <test> | |
41 <param name="input_type_selector" value="tsv"/> | |
42 <param name="blast_input" value="BlastnTsvToGff_In.tabular" ftype="tabular"/> | |
43 <output name="output" ftype="gff3" > | |
44 <assert_contents> | |
45 <has_line line="##gff-version 3"/> | |
46 <has_n_lines n="3152"/> | |
47 </assert_contents> | |
48 </output> | |
49 </test> | |
50 </tests> | |
51 <help><![CDATA[ | |
52 **What it does** | |
53 | |
54 Convert BlastN XML or tabular results into GFF3 format for visualization within JBrowse, please be sure to select the correct input option for your data. | |
55 This is critical for displaying the position of high-scoring pairs of the Target aligned against the Query. If you need to convert BlastP results, please use the "BlastP Results to GFF3" tool. | |
56 | |
57 ]]></help> | |
58 <expand macro="citations" /> | |
59 </tool> | |
60 |