Mercurial > repos > iuc > sarscov2formatter
comparison sarscov2formatter.xml @ 1:e3a7995dce75 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit 1bd215457a39296c069caa6be30939f4f1bdadeb"
author | iuc |
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date | Fri, 20 Nov 2020 18:21:33 +0000 |
parents | 1c664ff29354 |
children | 2e993ff8e7dc |
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0:1c664ff29354 | 1:e3a7995dce75 |
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1 <tool id="sarscov2formatter" name="sarscov2formatter" version="0.1" profile="18.01"> | 1 <tool id="sarscov2formatter" name="sarscov2formatter" version="0.5.3+galaxy1" profile="18.01"> |
2 <requirements> | 2 <requirements> |
3 <requirement type="package" version="0.5.2">sarscov2formatter</requirement> | 3 <requirement type="package" version="0.5.3">sarscov2formatter</requirement> |
4 </requirements> | 4 </requirements> |
5 <command><![CDATA[ | 5 <command><![CDATA[ |
6 sarscov2formatter | 6 sarscov2formatter |
7 -a $align | 7 -a '$align' |
8 #if $source.source_choice == 'ncbi': | 8 #if $source.source_choice == 'ncbi': |
9 -m ncbi | 9 -m ncbi |
10 #else: | 10 #else: |
11 -m '$source.meta' | 11 -m '$source.meta' |
12 #end if | 12 #end if |
18 <option value="ncbi">NCBI</option> | 18 <option value="ncbi">NCBI</option> |
19 <option value="other">Other</option> | 19 <option value="other">Other</option> |
20 </param> | 20 </param> |
21 <when value="ncbi" /> | 21 <when value="ncbi" /> |
22 <when value="other" > | 22 <when value="other" > |
23 <param name="meta" type="data" format='tabular' label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" /> | 23 <param name="meta" type="data" format="tabular" label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" /> |
24 </when> | 24 </when> |
25 </conditional> | 25 </conditional> |
26 </inputs> | 26 </inputs> |
27 <outputs> | 27 <outputs> |
28 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" /> | 28 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" /> |
29 <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" /> | 29 <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" /> |
30 <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" /> | 30 <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" /> |
31 </outputs> | 31 </outputs> |
32 <tests> | 32 <tests> |
33 <!-- note: test with ncbi yields unstable results for meta -> assert contents. | |
34 also needs a surprising amount memory (1.7G) which might | |
35 become impractival in the future --> | |
33 <test> | 36 <test> |
34 <param name="align" ftype="fasta" value="align.fasta" /> | 37 <param name="align" ftype="fasta" value="align.fasta" /> |
35 <param name="source_choice" value="ncbi" /> | 38 <param name="source_choice" value="ncbi" /> |
36 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" /> | 39 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" /> |
37 <output name="dups" ftype="json" compare="diff" value="dups.json" /> | 40 <output name="dups" ftype="json" compare="diff" value="dups.json" /> |
38 <output name="outmeta" ftype="json" compare="diff" value="meta.json" /> | 41 <output name="outmeta" ftype="json"> |
42 <assert_contents> | |
43 <has_line_matching expression="\{"/> | |
44 <has_line_matching expression="\}"/> | |
45 <has_text_matching expression='"LR757995": \{'/> | |
46 <has_text_matching expression='"collected": '/> | |
47 <has_text_matching expression='"collected": '/> | |
48 <has_text_matching expression='"location": '/> | |
49 <has_text_matching expression='"country": '/> | |
50 <has_text_matching expression='"locality": '/> | |
51 <has_text_matching expression='"state": '/> | |
52 <has_text_matching expression='"subregion": '/> | |
53 </assert_contents> | |
54 </output> | |
39 </test> | 55 </test> |
56 <!-- TODO test with tabular input, does not work yet | |
57 test.tsv has been generated with test.py | |
58 https://github.com/nickeener/sarscov2formatter/issues/2 --> | |
59 <!-- <test>--> | |
60 <!-- <param name="align" ftype="fasta" value="align.fasta" />--> | |
61 <!-- <conditional name="source" >--> | |
62 <!-- <param name="source_choice" value="other" />--> | |
63 <!-- <param name="meta" ftype="tabular" value="test.tsv" />--> | |
64 <!-- </conditional>--> | |
65 <!-- <output name="msa" ftype="fasta" compare="diff" value="msa-other.fasta" />--> | |
66 <!-- <output name="dups" ftype="json" compare="diff" value="dups-other.json" />--> | |
67 <!-- <output name="outmeta" ftype="json" compare="diff" value="meta-other.json" />--> | |
68 <!-- </test>--> | |
40 </tests> | 69 </tests> |
41 <help><![CDATA[ | 70 <help><![CDATA[ |
42 | 71 |
43 ================= | 72 ================= |
44 sarscov2formatter | 73 sarscov2formatter |