Mercurial > repos > iuc > krakentools_beta_diversity

comparison beta_diversity.xml @ 5:e1172268cc6b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 60eb96ad3ff782075ca1f29e26ffe5487bbb93ed
author iuc
date Fri, 22 Nov 2024 09:27:08 +0000
parents 56bf015afbd1
children
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4:ee324af0fcfd 5:e1172268cc6b
5 </macros> 5 </macros>
6 <expand macro="biotools"/> 6 <expand macro="biotools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="version"/> 8 <expand macro="version"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #import re
11 #set input_names=[]
12
13 #for $input in $inputs
14 #set identifier = re.sub('[^\s\w\-.]', '_', str($input.element_identifier))
15 #silent $input_names.append($identifier)
16 ln -s '$input' '${identifier}' &&
17 #end for
18
10 beta_diversity.py 19 beta_diversity.py
11 --inputs 20 --inputs
12 #for $input in $inputs 21 #for $input_name in $input_names
13 '$input' 22 '${input_name}'
14 #end for 23 #end for
15 --type '$sample.type' 24 --type '$sample.type'
16 #if $sample.type == 'kreport' 25 #if $sample.type == 'kreport'
17 --level '$sample.level' 26 --level '$sample.level'
18 #else if $sample.type == 'krona' 27 #else if $sample.type == 'krona'
41 </when> 50 </when>
42 </conditional> 51 </conditional>
43 52
44 </inputs> 53 </inputs>
45 <outputs> 54 <outputs>
46 <data name="output" format="txt" /> 55 <data name="output" format="tabular" />
47 </outputs> 56 </outputs>
48 <tests> 57 <tests>
49 <test> 58 <test>
50 <param name="inputs" value="beta_bracken_1.tabular,beta_bracken_2.tabular,beta_bracken_3.tabular"/> 59 <param name="inputs" value="beta_bracken_1.tabular,beta_bracken_2.tabular,beta_bracken_3.tabular"/>
51 <param name="type" value="bracken"/> 60 <param name="type" value="bracken"/>
52 <output name="output" ftype="txt"> 61 <output name="output" ftype="tabular">
53 <assert_contents> 62 <assert_contents>
63 <has_text_matching expression="#[012]&#9;beta_[a-z]+_[123].tabular \([0-9]+ reads\)" n="3"/>
64 <has_n_columns n="4" comment="#"/>
65 <has_n_lines n="7"/>
54 <has_text text="0.629"/> 66 <has_text text="0.629"/>
55 <has_text text="0.993"/>
56 <has_text text="0.995"/>
57 </assert_contents> 67 </assert_contents>
58 </output> 68 </output>
59 </test> 69 </test>
60 <test> 70 <test>
61 <param name="inputs" value="beta_kreport_1.tabular,beta_kreport_2.tabular,beta_kreport_3.tabular"/> 71 <param name="inputs" value="beta_kreport_1.tabular,beta_kreport_2.tabular,beta_kreport_3.tabular"/>
62 <param name="type" value="kreport"/> 72 <param name="type" value="kreport"/>
63 <output name="output" ftype="txt"> 73 <output name="output" ftype="tabular">
64 <assert_contents> 74 <assert_contents>
75 <has_text text="beta_kreport_1.tabular"/>
76 <has_text_matching expression="#[012]&#9;beta_[a-z]+_[123].tabular \([0-9]+ reads\)" n="3"/>
77 <has_n_columns n="4" comment="#"/>
78 <has_n_lines n="7"/>
65 <has_text text="0.584"/> 79 <has_text text="0.584"/>
66 <has_text text="0.996"/>
67 <has_text text="0.995"/>
68 </assert_contents> 80 </assert_contents>
69 </output> 81 </output>
70 </test> 82 </test>
71 <test> 83 <test>
72 <param name="inputs" value="beta_krona_1.tabular,beta_krona_2.tabular"/> 84 <param name="inputs" value="beta_krona_1.tabular,beta_krona_2.tabular"/>
73 <param name="type" value="krona"/> 85 <param name="type" value="krona"/>
74 <param name="level" value="G"/> 86 <param name="level" value="G"/>
75 <output name="output" ftype="txt"> 87 <output name="output" ftype="tabular">
76 <assert_contents> 88 <assert_contents>
89 <has_text_matching expression="#[01]&#9;beta_[a-z]+_[12].tabular \([0-9]+ reads\)" n="2"/>
90 <has_n_columns n="3" comment="#"/>
91 <has_n_lines n="5"/>
77 <has_text text="0.993"/> 92 <has_text text="0.993"/>
78 </assert_contents> 93 </assert_contents>
79 </output> 94 </output>
80 </test> 95 </test>
81 </tests> 96 </tests>