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comparison sarscov2formatter.xml @ 2:2e993ff8e7dc draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter commit dc4d978a42ef881f602b813f9416fd37e3ea3b6a"
author iuc
date Mon, 22 Nov 2021 10:41:59 +0000
parents e3a7995dce75
children
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1:e3a7995dce75 2:2e993ff8e7dc
1 <tool id="sarscov2formatter" name="sarscov2formatter" version="0.5.3+galaxy1" profile="18.01"> 1 <tool id="sarscov2formatter" name="sarscov2formatter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
2 <macros>
3 <token name="@TOOL_VERSION@">1.0</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros>
2 <requirements> 6 <requirements>
3 <requirement type="package" version="0.5.3">sarscov2formatter</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">sarscov2formatter</requirement>
4 </requirements> 8 </requirements>
5 <command><![CDATA[ 9 <command><![CDATA[
6 sarscov2formatter 10 sarscov2formatter
7 -a '$align' 11 -a '$align'
8 #if $source.source_choice == 'ncbi': 12 #if $source.source_choice == 'ncbi':
9 -m ncbi 13 #if $source.meta
14 -n '$source.meta'
15 #end if
10 #else: 16 #else:
11 -m '$source.meta' 17 -m '$source.meta'
12 #end if 18 #end if
13 ]]></command> 19 ]]></command>
14 <inputs> 20 <inputs>
16 <conditional name="source" > 22 <conditional name="source" >
17 <param name="source_choice" type="select" label="NCBI datasource or other?" > 23 <param name="source_choice" type="select" label="NCBI datasource or other?" >
18 <option value="ncbi">NCBI</option> 24 <option value="ncbi">NCBI</option>
19 <option value="other">Other</option> 25 <option value="other">Other</option>
20 </param> 26 </param>
21 <when value="ncbi" /> 27 <when value="ncbi">
28 <param name="meta" type="data" format="json" optional="true" label="Metadata from NCBI" help="If not given it will be downloaded" />
29 </when>
22 <when value="other" > 30 <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)" /> 31 <param name="meta" type="data" format="tabular" label="Metadata" help="Tabular file with metadata with the correct columns (see below)" />
24 </when> 32 </when>
25 </conditional> 33 </conditional>
26 </inputs> 34 </inputs>
27 <outputs> 35 <outputs>
28 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" /> 36 <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" />
29 <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" /> 37 <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" />
30 <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" /> 38 <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" />
31 </outputs> 39 </outputs>
32 <tests> 40 <tests>
33 <!-- note: test with ncbi yields unstable results for meta -> assert contents. 41 <!-- 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 -->
36 <test> 42 <test>
37 <param name="align" ftype="fasta" value="align.fasta" /> 43 <param name="align" ftype="fasta" value="align.fasta" />
38 <param name="source_choice" value="ncbi" /> 44 <conditional name="source" >
45 <param name="source_choice" value="ncbi" />
46 </conditional>
39 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" /> 47 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" />
40 <output name="dups" ftype="json" compare="diff" value="dups.json" /> 48 <output name="dups" ftype="json" compare="diff" value="dups.json" />
41 <output name="outmeta" ftype="json"> 49 <output name="outmeta" ftype="json">
42 <assert_contents> 50 <assert_contents>
43 <has_line_matching expression="\{"/> 51 <has_line_matching expression="\{"/>
51 <has_text_matching expression='"state": '/> 59 <has_text_matching expression='"state": '/>
52 <has_text_matching expression='"subregion": '/> 60 <has_text_matching expression='"subregion": '/>
53 </assert_contents> 61 </assert_contents>
54 </output> 62 </output>
55 </test> 63 </test>
56 <!-- TODO test with tabular input, does not work yet 64 <!-- test with local NCBI data, here a json file containing only the entries relevant for the fasta -->
57 test.tsv has been generated with test.py 65 <test>
58 https://github.com/nickeener/sarscov2formatter/issues/2 --> 66 <param name="align" ftype="fasta" value="align.fasta" />
59 <!-- <test>--> 67 <conditional name="source" >
60 <!-- <param name="align" ftype="fasta" value="align.fasta" />--> 68 <param name="source_choice" value="ncbi" />
61 <!-- <conditional name="source" >--> 69 <param name="meta" ftype="json" value="test.json" />
62 <!-- <param name="source_choice" value="other" />--> 70 </conditional>
63 <!-- <param name="meta" ftype="tabular" value="test.tsv" />--> 71 <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" />
64 <!-- </conditional>--> 72 <output name="dups" ftype="json" compare="diff" value="dups.json" />
65 <!-- <output name="msa" ftype="fasta" compare="diff" value="msa-other.fasta" />--> 73 <output name="outmeta" ftype="json">
66 <!-- <output name="dups" ftype="json" compare="diff" value="dups-other.json" />--> 74 <assert_contents>
67 <!-- <output name="outmeta" ftype="json" compare="diff" value="meta-other.json" />--> 75 <has_line_matching expression="\{"/>
68 <!-- </test>--> 76 <has_line_matching expression="\}"/>
77 <has_text_matching expression='"LR757995": \{'/>
78 <has_text_matching expression='"collected": '/>
79 <has_text_matching expression='"collected": '/>
80 <has_text_matching expression='"location": '/>
81 <has_text_matching expression='"country": '/>
82 <has_text_matching expression='"locality": '/>
83 <has_text_matching expression='"state": '/>
84 <has_text_matching expression='"subregion": '/>
85 </assert_contents>
86 </output>
87 </test>
88 <!-- TODO test with tabular input -->
89 <test>
90 <param name="align" ftype="fasta" value="align.fasta" />
91 <conditional name="source" >
92 <param name="source_choice" value="other" />
93 <param name="meta" ftype="tabular" value="test.tsv" />
94 </conditional>
95 <output name="msa" ftype="fasta" compare="diff" value="msa-other.fasta" />
96 <output name="dups" ftype="json" compare="diff" value="dups-other.json" />
97 <output name="outmeta" ftype="json" compare="diff" value="meta-other.json" />
98 </test>
69 </tests> 99 </tests>
70 <help><![CDATA[ 100 <help><![CDATA[
71 101
72 ================= 102 =================
73 sarscov2formatter 103 sarscov2formatter
74 ================= 104 =================
75 105
76 Custom sript that performs necessary formatting operations for the SARS-CoV2 Selection Analysis workflow. 106 Custom sript that performs necessary formatting operations for the SARS-CoV2 Selection Analysis workflow.
77 107
108 If using NCBI as data source the file can be obtained from https://www.ncbi.nlm.nih.gov/projects/genome/sars-cov-2-seqs/ncov-sequences.yaml.
109 If not given the tool will download it automatically.
110
78 If using non-NCBI data, the metadata input file must be tabular with the following columns: ID, collection_date, country, state (optional), and locality (optional). Optional columns should still be created even if they are not used. 111 If using non-NCBI data, the metadata input file must be tabular with the following columns: ID, collection_date, country, state (optional), and locality (optional). Optional columns should still be created even if they are not used.
79 112
80 Dates should be of the format: YYMMDD (example: May 1 2020 = 20200501). 113 Dates should be of the format: YYMMDD (example: May 1 2020 = 20200501).
81
82 114
83 ]]></help> 115 ]]></help>
84 <citations> 116 <citations>
85 <citation type="bibtex"> 117 <citation type="bibtex">
86 @misc{githubsarscov2formatter, 118 @misc{githubsarscov2formatter,