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comparison macros.xml @ 0:1a7773882d2c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 800d16f3bd40266d8734f4572988cb2b306b4fd3"
author iuc
date Thu, 27 Jan 2022 08:20:47 +0000
parents
children e34fcd410816
comparison
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-1:000000000000 0:1a7773882d2c
1 <macros>
2 <token name="@TOOL_VERSION@">12.27.1</token>
3 <token name="@PROFILE@">20.01</token>
4 <token name="@LICENSE@">MIT</token>
5 <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
6 <token name="@SETUP_CERTIFICATES@"><![CDATA[
7 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates
8 [ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
9 ]]></token>
10 <xml name="requirements">
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
13 <requirement type="package" version="2021.5.30">ca-certificates</requirement>
14 <requirement type="package" version="16.02">p7zip</requirement>
15 </requirements>
16 </xml>
17 <xml name="annotation">
18 <param argument="--annotated" type="boolean" truevalue="--annotated" falsevalue="" label="Only include genomes with annotation ?"/>
19 </xml>
20 <xml name="dehydrated">
21 <param argument="--dehydrated" type="boolean" truevalue="--dehydrated" falsevalue="" label="Download a dehydrated zip archive including the data report and locations of data files ?" help="Use the rehydrate tools to retrieve data files"/>
22 </xml>
23 <xml name="assembly_level">
24 <param argument="--assembly-level" type="select" label="Restrict assemblies to a comma-separated list of one or more of these" multiple="true" optional="true">
25 <option value="chromosome">Chromosome</option>
26 <option value="complete_genome">Complete Genome</option>
27 <option value="contig">Contig</option>
28 <option value="scaffold">Scaffold</option>
29 </param>
30 </xml>
31 <xml name="assembly_source">
32 <param argument="--assembly-source" type="select" optional="true">
33 <option value="refseq">RefSeq</option>
34 <option value="genabnk">GenBank</option>
35 </param>
36 </xml>
37 <xml name="text_or_file" token_what="accession" token_what_extended="NCBI Assembly accession" token_help="Can be NCBI Assembly or BioProject accession">
38 <conditional name="text_or_file" label="How do you want to specify the @WHAT@(s) to download">
39 <param name="text_or_file" type="select" label="Enter @WHAT@ or read from file ?">
40 <option value="text">Enter @WHAT@s</option>
41 <option value="file">Read a list of @WHAT_EXTENDED@s from a dataset</option>
42 </param>
43 <when value="text">
44 <param name="accession" type="text" label="Enter space separated list of @WHAT@s" help="@HELP@">
45 <yield/>
46 </param>
47 </when>
48 <when value="file">
49 <param argument="--inputfile" type="data" format="txt" label="Select dataset with list of @WHAT_EXTENDED@s" help="@HELP@"/>
50 </when>
51 </conditional>
52 </xml>
53 <xml name="chromosomes">
54 <param argument="--chromosomes" type="text" label="Limit chromosomes to a comma-delimited list of chromosomes">
55 <sanitizer invalid_char="">
56 <valid initial="string.letters,string.digits">
57 <add value="_" />
58 <add value="." />
59 <add value="," />
60 </valid>
61 </sanitizer>
62 </param>
63 </xml>
64 <xml name="include" token_include_what="gbff" token_include_label="Include GenBank flat file sequence and annotation, if available">
65 <param argument="--include-@INCLUDE_WHAT@" type="boolean" truevalue="--include-@INCLUDE_WHAT@" falsevalue="" label="@INCLUDE_LABEL@" />
66 </xml>
67 <xml name="includes_genome">
68 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation, if available"/>
69 <expand macro="include" include_what="gtf" include_label="Include gtf annotation file, if available"/>
70 </xml>
71 <xml name="exclude" token_exclude_what="gff3" token_exclude_label="Exclude gff3 annotation file">
72 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" truevalue="--exclude-@EXCLUDE_WHAT@" falsevalue="" label="@EXCLUDE_LABEL@" />
73 </xml>
74 <xml name="anti-exclude" token_exclude_what="gff3" token_exclude_label="Include gff3 annotation file" token_checked="false">
75 <param argument="--exclude-@EXCLUDE_WHAT@" type="boolean" falsevalue="--exclude-@EXCLUDE_WHAT@" truevalue="" label="@EXCLUDE_LABEL@" checked="@CHECKED@"/>
76 </xml>
77 <xml name="excludes_genome">
78 <expand macro="anti-exclude" exclude_what="seq" exclude_label="Include genomic sequence file" checked="true"/>
79 <expand macro="anti-exclude" exclude_what="gff3" exclude_label="Include gff3 annotation file"/>
80 <expand macro="anti-exclude" exclude_what="genomic-cds" exclude_label="Include cds from genomic sequence file"/>
81 <expand macro="anti-exclude" exclude_what="protein" exclude_label="Include protein sequence file"/>
82 <expand macro="anti-exclude" exclude_what="rna" exclude_label="Include transcript sequence file"/>
83 </xml>
84 <xml name="excludes_gene">
85 <expand macro="exclude" exclude_what="gene" exclude_label="Exclude gene sequence file"/>
86 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
87 <expand macro="exclude" exclude_what="rna" exclude_label="Exclude transcript sequence file"/>
88 </xml>
89 <xml name="excludes_virus_protein">
90 <yield/>
91 <expand macro="exclude" exclude_what="protein" exclude_label="Exclude protein sequence file"/>
92 <expand macro="exclude" exclude_what="pdb" exclude_label="Exclude protein structure files (pdb)"/>
93 <expand macro="exclude" exclude_what="gpff" exclude_label="Exclude protein sequence and annotation in GenPept flat file"/>
94 <expand macro="exclude" exclude_what="cds" exclude_label="Exclude CDS sequence file"/>
95 </xml>
96 <xml name="excludes_virus_genome">
97 <expand macro="excludes_virus_protein">
98 <expand macro="exclude" exclude_what="seq" exclude_label="Exclude genomic sequence file"/>
99 </expand>
100 </xml>
101 <token name="@EXCLUDES_GENOME@">$file_choices.exclude_gff3 $file_choices.exclude_genomic_cds $file_choices.exclude_protein $file_choices.exclude_rna $file_choices.exclude_seq</token>
102 <token name="@EXCLUDES_GENE@">$exclude_gene $exclude_protein $exclude_rna</token>
103 <token name="@EXCLUDES_VIRUS_PROTEIN@">$exclude_protein $exclude_pdb $exclude_gpff $exclude_cds</token>
104 <token name="@EXCLUDES_VIRUS_GENOME@">$exclude_seq @EXCLUDES_VIRUS_PROTEIN@</token>
105 <xml name="includes_virus_genome">
106 <expand macro="include" include_what="gbff" include_label="Include GenBank flat file sequence and annotation"/>
107 </xml>
108 <token name="@INCLUDES_GENOME@">$file_choices.include_gbff $file_choices.include_gtf</token>
109 <token name="@INCLUDES_VIRUS_GENOME@">$include_gbff</token>
110 <xml name="released_options" token_released_what="genomes" token_before_or_after="before">
111 <param argument="--released-@BEFORE_OR_AFTER@" type="text" optional="true" label="Only include @RELEASED_WHAT@ that have been released @BEFORE_OR_AFTER@ a specified date (MM/DD/YYYY)"></param>
112 </xml>
113 <token name="@RELEASED_BEFORE@">#if $filters.released_before:
114 --released-before '$filters.released_before'
115 #end if
116 </token>
117 <token name="@RELEASED_SINCE@">#if $filters.released_since:
118 --released-since '$filters.released_since'
119 #end if
120 </token>
121 </macros>