Mercurial > repos > iuc > omark
comparison omark.xml @ 0:ce13b4c42256 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
author | iuc |
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date | Wed, 21 Feb 2024 19:27:16 +0000 |
parents | |
children | 2eebe7f521f3 |
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1 <?xml version="1.0"?> | |
2 <tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy0" profile="21.05"> | |
3 <description>proteome quality assessment</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <requirements> | |
8 <expand macro="requirements" /> | |
9 </requirements> | |
10 | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 omamer search --db '$database' --query '$input' --out 'output_omamer' | |
13 && | |
14 | |
15 omark | |
16 -f 'output_omamer' | |
17 -d '$database' | |
18 $omark_mode | |
19 -i '$input_iso' | |
20 -t 't' | |
21 -r 'r' | |
22 -o omark_galaxy | |
23 | |
24 ]]></command> | |
25 | |
26 <inputs> | |
27 <param name="input" type="data" format="fasta" label="Protein sequences"/> | |
28 <param name="input_iso" type="data" format="txt" optional="true" label="Input isoform file" help="A semi-colon separated file, listing all isoforms of each genes, with one gene per line."/> | |
29 <param argument="-c" name="omark_mode" type="boolean" checked="false" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/> | |
30 <param name="database" label="OMAmer database" type="select"> | |
31 <options from_data_table="omamer"/> | |
32 </param> | |
33 | |
34 <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome"> | |
35 <sanitizer invalid_char=""> | |
36 <valid initial="string.letters,string.digits"> | |
37 <add value="_" /> | |
38 </valid> | |
39 </sanitizer> | |
40 <validator type="regex">[0-9a-zA-Z_]+</validator> | |
41 </param> | |
42 <param argument="-r" type="text" optional="true" label="Taxonomic rank"> | |
43 <sanitizer invalid_char=""> | |
44 <valid initial="string.letters,string.digits"> | |
45 <add value="_" /> | |
46 </valid> | |
47 </sanitizer> | |
48 <validator type="regex">[0-9a-zA-Z_]+</validator> | |
49 </param> | |
50 | |
51 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> | |
52 <option value="detail_sum" selected="true">Detailed summary</option> | |
53 <option value="hog">HOG identifiers</option> | |
54 <option value="pdf">PDF Graphic representation </option> | |
55 <option value="png">PNG Graphic representation </option> | |
56 <option value="sum">Comparative proteome analysis</option> | |
57 <option value="tax">Taxomony</option> | |
58 <option value="ump">Protein identifiers</option> | |
59 </param> | |
60 </inputs> | |
61 | |
62 <outputs> | |
63 <data name="omark_detail_sum" format="txt" label="${tool.name} on ${on_string}: Detailed summary" from_work_dir="omark_galaxy/*detailed_summary.txt"> | |
64 <filter>outputs and 'detail_sum' in outputs</filter> | |
65 </data> | |
66 <data name="omark_hog" format="omq" label="${tool.name} on ${on_string}: HOG identifiers" from_work_dir="omark_galaxy/*.omq"> | |
67 <filter>outputs and 'hog' in outputs</filter> | |
68 </data> | |
69 <data name="omark_pdf" format="pdf" label="${tool.name} on ${on_string}: Graphic representation (pdf)" from_work_dir="omark_galaxy/*.pdf"> | |
70 <filter>outputs and 'pdf' in outputs</filter> | |
71 </data> | |
72 <data name="omark_png" format="png" label="${tool.name} on ${on_string}: Graphic representation (png)" from_work_dir="omark_galaxy/*.png"> | |
73 <filter>outputs and 'png' in outputs</filter> | |
74 </data> | |
75 <data name="omark_sum" format="sum" label="${tool.name} on ${on_string}: Comparative proteome analysis" from_work_dir="omark_galaxy/*.sum"> | |
76 <filter>outputs and 'sum' in outputs</filter> | |
77 </data> | |
78 <data name="omark_tax" format="txt" label="${tool.name} on ${on_string}: Taxomony" from_work_dir="omark_galaxy/*.tax"> | |
79 <filter>outputs and 'tax' in outputs</filter> | |
80 </data> | |
81 <data name="omark_ump" format="ump" label="${tool.name} on ${on_string}: Protein identifiers" from_work_dir="omark_galaxy/*.ump"> | |
82 <filter>outputs and 'ump' in outputs</filter> | |
83 </data> | |
84 </outputs> | |
85 | |
86 <tests> | |
87 <test expect_failure="true"> | |
88 <param name="input" value="input.fasta"/> | |
89 <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/> | |
90 <param name="database" value="test"/> | |
91 </test> | |
92 </tests> | |
93 | |
94 | |
95 <help><![CDATA[ | |
96 OMark_: is a software for proteome quality assessment. | |
97 It provides measures of proteome completeness, characterizes the consistency | |
98 of all protein coding genes with regard to their homologs, and identifies the | |
99 presence of contamination from other species. | |
100 | |
101 OMArk relies on the OMA orthology database. | |
102 For more information, please refer to the OMamer_ documentaion. | |
103 | |
104 .. _OMark: https://github.com/DessimozLab/OMArk | |
105 .. _OMamer: https://github.com/DessimozLab/omamer | |
106 ]]></help> | |
107 <expand macro="citation"/> | |
108 </tool> |