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comparison omark.xml @ 0:ff07b7d62944 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
author iuc
date Fri, 14 Mar 2025 10:03:31 +0000
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-1:000000000000 0:ff07b7d62944
1 <?xml version="1.0"?>
2 <tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
3 <description>proteome quality assessment</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">omark</xref>
9 </xrefs>
10 <requirements>
11 <expand macro="requirements" />
12 </requirements>
13
14 <command detect_errors="exit_code"><![CDATA[
15 omamer search --db '$database.fields.path' --query '$input' --out 'output_omamer'
16
17 &&
18
19 omark
20 -f 'output_omamer'
21 -d '$database.fields.path'
22 $omark_mode
23
24 #if $input_iso:
25 -i '$input_iso'
26 #end if
27
28 #if $t:
29 -t '$t'
30 #end if
31
32 #if $r:
33 -r '$r'
34 #end if
35
36 -o omark_galaxy
37 ]]></command>
38
39 <inputs>
40 <param name="input" type="data" format="fasta" label="Protein sequences"/>
41 <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."/>
42 <param argument="-c" name="omark_mode" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/>
43 <param name="database" label="OMAmer database" type="select">
44 <options from_data_table="omamer"/>
45 </param>
46
47 <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome">
48 <sanitizer invalid_char="">
49 <valid initial="string.letters,string.digits">
50 <add value="_" />
51 </valid>
52 </sanitizer>
53 <validator type="regex">[0-9a-zA-Z_]+</validator>
54 </param>
55 <param argument="-r" type="text" optional="true" label="Taxonomic rank">
56 <sanitizer invalid_char="">
57 <valid initial="string.letters,string.digits">
58 <add value="_" />
59 </valid>
60 </sanitizer>
61 <validator type="regex">[0-9a-zA-Z_]+</validator>
62 </param>
63
64 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
65 <option value="detail_sum" selected="true">Detailed summary</option>
66 <option value="hog">HOG identifiers</option>
67 <option value="pdf">PDF Graphic representation </option>
68 <option value="png">PNG Graphic representation </option>
69 <option value="sum">Comparative proteome analysis</option>
70 <option value="tax">Taxomony</option>
71 <option value="ump">Protein identifiers</option>
72 </param>
73 </inputs>
74
75 <outputs>
76 <data name="omark_detail_sum" format="txt" label="${tool.name} on ${on_string}: Detailed summary" from_work_dir="omark_galaxy/*detailed_summary.txt">
77 <filter>outputs and 'detail_sum' in outputs</filter>
78 </data>
79 <data name="omark_hog" format="omq" label="${tool.name} on ${on_string}: HOG identifiers" from_work_dir="omark_galaxy/*.omq">
80 <filter>outputs and 'hog' in outputs</filter>
81 </data>
82 <data name="omark_pdf" format="pdf" label="${tool.name} on ${on_string}: Graphic representation (pdf)" from_work_dir="omark_galaxy/*.pdf">
83 <filter>outputs and 'pdf' in outputs</filter>
84 </data>
85 <data name="omark_png" format="png" label="${tool.name} on ${on_string}: Graphic representation (png)" from_work_dir="omark_galaxy/*.png">
86 <filter>outputs and 'png' in outputs</filter>
87 </data>
88 <data name="omark_sum" format="sum" label="${tool.name} on ${on_string}: Comparative proteome analysis" from_work_dir="omark_galaxy/*.sum">
89 <filter>outputs and 'sum' in outputs</filter>
90 </data>
91 <data name="omark_tax" format="txt" label="${tool.name} on ${on_string}: Taxomony" from_work_dir="omark_galaxy/*.tax">
92 <filter>outputs and 'tax' in outputs</filter>
93 </data>
94 <data name="omark_ump" format="ump" label="${tool.name} on ${on_string}: Protein identifiers" from_work_dir="omark_galaxy/*.ump">
95 <filter>outputs and 'ump' in outputs</filter>
96 </data>
97 </outputs>
98
99 <tests>
100 <test expect_failure="true">
101 <param name="input" value="input.fasta"/>
102 <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/>
103 <param name="database" value="test"/>
104
105 <!-- Couldn't create a minimal working hdf5 dataset -->
106 <assert_stderr>
107 <has_text text="file signature not found"/>
108 <has_text text="End of HDF5 error back trace" />
109 </assert_stderr>
110 </test>
111 </tests>
112
113
114 <help><![CDATA[
115 OMark_: is a software for proteome quality assessment.
116 It provides measures of proteome completeness, characterizes the consistency
117 of all protein coding genes with regard to their homologs, and identifies the
118 presence of contamination from other species.
119
120 OMArk relies on the OMA orthology database.
121 For more information, please refer to the OMamer_ documentaion.
122
123 .. _OMark: https://github.com/DessimozLab/OMArk
124 .. _OMamer: https://github.com/DessimozLab/omamer
125 ]]></help>
126 <expand macro="citation"/>
127 </tool>