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comparison omark.xml @ 1:2eebe7f521f3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 839a3c8e9b651fbc0f4fefdd79ce1545a257cb0f
author iuc
date Thu, 07 Mar 2024 18:22:16 +0000
parents ce13b4c42256
children 9607b69326e1
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0:ce13b4c42256 1:2eebe7f521f3
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy0" profile="21.05"> 2 <tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
3 <description>proteome quality assessment</description> 3 <description>proteome quality assessment</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 </requirements> 9 </requirements>
10 10
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 omamer search --db '$database' --query '$input' --out 'output_omamer' 12 omamer search --db '$database.fields.path' --query '$input' --out 'output_omamer'
13
13 && 14 &&
14 15
15 omark 16 omark
16 -f 'output_omamer' 17 -f 'output_omamer'
17 -d '$database' 18 -d '$database.fields.path'
18 $omark_mode 19 $omark_mode
19 -i '$input_iso' 20 -i '$input_iso'
20 -t 't' 21 -t '$t'
21 -r 'r' 22 -r '$r'
22 -o omark_galaxy 23 -o omark_galaxy
23 24
24 ]]></command> 25 ]]></command>
25 26
26 <inputs> 27 <inputs>
27 <param name="input" type="data" format="fasta" label="Protein sequences"/> 28 <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 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 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"/>
30 <param name="database" label="OMAmer database" type="select"> 31 <param name="database" label="OMAmer database" type="select">
31 <options from_data_table="omamer"/> 32 <options from_data_table="omamer"/>
32 </param> 33 </param>
33 34
34 <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome"> 35 <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome">
45 <add value="_" /> 46 <add value="_" />
46 </valid> 47 </valid>
47 </sanitizer> 48 </sanitizer>
48 <validator type="regex">[0-9a-zA-Z_]+</validator> 49 <validator type="regex">[0-9a-zA-Z_]+</validator>
49 </param> 50 </param>
50 51
51 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> 52 <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="detail_sum" selected="true">Detailed summary</option>
53 <option value="hog">HOG identifiers</option> 54 <option value="hog">HOG identifiers</option>
54 <option value="pdf">PDF Graphic representation </option> 55 <option value="pdf">PDF Graphic representation </option>
55 <option value="png">PNG Graphic representation </option> 56 <option value="png">PNG Graphic representation </option>
86 <tests> 87 <tests>
87 <test expect_failure="true"> 88 <test expect_failure="true">
88 <param name="input" value="input.fasta"/> 89 <param name="input" value="input.fasta"/>
89 <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/> 90 <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/>
90 <param name="database" value="test"/> 91 <param name="database" value="test"/>
92
93 <!-- Couldn't create a minimal working hdf5 dataset -->
94 <assert_stderr>
95 <has_text text="file signature not found"/>
96 <has_text text="End of HDF5 error back trace" />
97 </assert_stderr>
91 </test> 98 </test>
92 </tests> 99 </tests>
93 100
94 101
95 <help><![CDATA[ 102 <help><![CDATA[
96 OMark_: is a software for proteome quality assessment. 103 OMark_: is a software for proteome quality assessment.
97 It provides measures of proteome completeness, characterizes the consistency 104 It provides measures of proteome completeness, characterizes the consistency
98 of all protein coding genes with regard to their homologs, and identifies the 105 of all protein coding genes with regard to their homologs, and identifies the
99 presence of contamination from other species. 106 presence of contamination from other species.
100 107
101 OMArk relies on the OMA orthology database. 108 OMArk relies on the OMA orthology database.
102 For more information, please refer to the OMamer_ documentaion. 109 For more information, please refer to the OMamer_ documentaion.
103 110
104 .. _OMark: https://github.com/DessimozLab/OMArk 111 .. _OMark: https://github.com/DessimozLab/OMArk