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comparison krona_mothur.xml @ 0:607c5e7e0a64 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
author erasmus-medical-center
date Wed, 13 Dec 2017 10:09:50 -0500
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-1:000000000000 0:607c5e7e0a64
1 <tool id="mycrobiota-krona-mothur" name="Krona" version="1">
2 <description>for mothur datasets</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="2.7">krona</requirement>
8 </requirements>
9 <command detect_errors="aggressive"><![CDATA[
10 ## create symlinks to taxonomy files for nicer display names in output
11 #if $input.haveshared == 'no':
12 #for $tax in $input.taxonomy:
13 ln -s '$tax' '$tax.name' &&
14 #end for
15 #end if
16
17 python '$__tool_directory__/mycrobiota.py'
18 #if $input.haveshared == 'yes':
19 --command create_krona_plot_multisample
20 --shared_file '$input.shared_file'
21 #if $input.level == 'None':
22 --level '$input.taxonomy.name'
23 #else:
24 --level '$input.level'
25 #end if
26 --taxonomy $input.taxonomy
27 #else:
28 --command create_krona_plot
29 #for $tax in $input.taxonomy:
30 --taxonomy '$tax.name'
31 #end for
32 #end if
33 ${with_otu}
34 ]]></command>
35 <inputs>
36 <conditional name="input">
37 <param name="haveshared" type="select" label="Would you like to supply a mothur shared file?"
38 help="This will create a multisample plot. If you select 'no', you can still create a multisample plot by providing a taxonomy file per sample">
39 <option value="no">No</option>
40 <option value="yes">Yes</option>
41 </param>
42 <when value="no">
43 <param argument="--taxonomy" type="data" multiple="true" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/>
44 </when>
45 <when value="yes">
46 <param argument="--taxonomy" type="data" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/>
47 <param argument="--shared_file" type="data" optional="true" format="mothur.shared" label="Supply a mothur shared file" help=""/>
48 <param argument="--level" type="select" optional="true" label="label - pick (one) OTU Label" help="leave blank for collections, will try to determine level from element names">
49 <options>
50 <filter type="data_meta" ref="shared_file" key="labels"/>
51 </options>
52 </param>
53 </when>
54 </conditional>
55 <param argument="--with_otu" type="boolean" checked="false" truevalue="--with-otu" falsevalue="" label="differentiate between different OTUs of same taxonomy?" help=""/>
56 </inputs>
57 <outputs>
58 <data name="krona_plot" format="html" from_work_dir="text.krona.html" label="Krona plot of ${on_string}: HTML"/>
59 </outputs>
60 <tests>
61 <test> <!-- test single sample -->
62 <param name="haveshared" value="no"/>
63 <param name="taxonomy" value="multisample.taxonomy"/>
64 <param name="with_otu" value="--with-otu"/>
65 <output name="krona_plot">
66 <assert_contents>
67 <has_text text="Krona"/>
68 <has_text text="Actinobacteria"/>
69 <not_has_text text="F3D0"/>
70 <not_has_text text="F3D148"/>
71 <not_has_text text="krona.test1.mothur.cons"/>
72 <has_text text="Otu0127"/>
73 </assert_contents>
74 </output>
75 </test>
76 <test> <!-- test multi samples (multiple single-sample taxonomy files) -->
77 <param name="haveshared" value="no"/>
78 <param name="taxonomy" value="multisample.taxonomy,krona.test1.mothur.cons.taxonomy"/>
79 <param name="with_otu" value=""/>
80 <output name="krona_plot">
81 <assert_contents>
82 <has_text text="Krona"/>
83 <has_text text="krona.test1.mothur.cons"/>
84 <has_text text="Actinobacteria"/>
85 <not_has_text text="F3D0"/>
86 <not_has_text text="F3D148"/>
87 <not_has_text text="Otu0127"/>
88 </assert_contents>
89 </output>
90 </test>
91 <test> <!-- test multi sample (single multisample taxonomy file with shared file) -->
92 <param name="haveshared" value="yes"/>
93 <param name="taxonomy" value="multisample.taxonomy"/>
94 <param name="shared_file" ftype="mothur.shared" value="example.mothur.shared"/>
95 <param name="with_otu" value="--with-otu"/>
96 <param name="level" value="0.03"/>
97 <output name="krona_plot">
98 <assert_contents>
99 <has_text text="Krona"/>
100 <has_text text="Actinobacteria"/>
101 <has_text text="F3D0"/>
102 <has_text text="F3D148"/>
103 </assert_contents>
104 </output>
105 </test>
106 </tests>
107 <help><![CDATA[
108 **What it does**
109 ]]></help>
110 <expand macro="citations">
111 <citation type="doi">10.1007/978-1-4614-6418-1_802-1</citation>
112 </expand>
113 </tool>