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comparison indicator.xml @ 0:10ae17108e85 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:36:02 -0400
parents
children 95175e14cc16
comparison
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-1:000000000000 0:10ae17108e85
1 <tool profile="16.07" id="mothur_indicator" name="Indicator" version="@WRAPPER_VERSION@.0">
2 <description>Identify indicator "species" for nodes on a tree</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat &&
11 #if $withdesign.tree:
12 ln -s "$withdesign.tree" withdesign.tree.dat &&
13 #end if
14 #if $withdesign.havedesign == "yes":
15 ln -s "$withdesign.design" withdesign.design.dat &&
16 #end if
17
18 echo 'indicator(
19 #if $withdesign.tree:
20 tree=withdesign.tree.dat,
21 #end if
22 #if $otu.is_of_type("mothur.relabund"):
23 relabund=otu.dat,
24 #elif $otu.is_of_type("mothur.shared"):
25 shared=otu.dat,
26 #end if
27 #if $label:
28 label=${ str($label).replace(",","-") },
29 #end if
30 #if $withdesign.groups:
31 groups=${ str($withdesign.groups).replace(",","-") },
32 #end if
33 #if $withdesign.havedesign == "yes":
34 design=withdesign.design.dat,
35 #end if
36 processors='\${GALAXY_SLOTS:-8}'
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 ]]></command>
41 <inputs>
42 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/>
43 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels">
44 <expand macro="labeloptions"/>
45 </param>
46 <conditional name="withdesign">
47 <param name="havedesign" type="select" label="Will you supply a design file?">
48 <option value="yes">yes</option>
49 <option value="no">no</option>
50 </param>
51 <when value="yes">
52 <param name="tree" type="data" format="tree" optional="true" label="tree - A newick-formatted tree" help="Optional, if a design file is provided."/>
53 <param name="design" type="data" format="mothur.design" optional="true" label="design - assign groups to new grouping" help="make sure your file is of type mothur.design. Design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
54 <param name="groups" type="select" optional="true" multiple="true" label="groups - Pick groups to annalyze">
55 <options>
56 <filter type="data_meta" ref="design" key="groups"/>
57 </options>
58 </param>
59 </when>
60 <when value="no">
61 <param name="tree" type="data" format="tree" label="tree - A newick-formatted tree" help="Mandatory if no design file is provided"/>
62 <param name="groups" type="select" optional="true" multiple="true" label="groups - Pick groups to annalyze">
63 <options>
64 <filter type="data_meta" ref="otu" key="groups"/>
65 </options>
66 </param>
67 </when>
68 </conditional>
69 </inputs>
70 <outputs>
71 <expand macro="logfile-output"/>
72 <data name="tree_out" format="mothur.tre" from_work_dir="withdesign.tree*.tre" label="${tool.name} on ${on_string}: indicator.tre">
73 <filter>tree</filter>
74 </data>
75 <data name="summary" format="tabular" from_work_dir="otu*.summary" label="${tool.name} on ${on_string}: indicator.summary"/>
76 </outputs>
77 <tests>
78 <test><!-- test with design input -->
79 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
80 <param name="havedesign" value="yes"/>
81 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
82 <param name="label" value="0.03"/>
83 <param name="groups" value="tardis,dalek"/>
84 <output name="summary">
85 <assert_contents>
86 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
87 <has_text text="forest"/>
88 <has_text text="pasture"/>
89 </assert_contents>
90 </output>
91 <expand macro="logfile-test"/>
92 </test>
93 <test><!-- test with design input and subset of groups-->
94 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
95 <param name="havedesign" value="yes"/>
96 <param name="design" value="toymothur.design2" ftype="mothur.design"/>
97 <param name="groups" value="tardis"/>
98 <output name="summary">
99 <assert_contents>
100 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
101 <has_text text="forest"/>
102 <not_has_text text="pasture"/>
103 </assert_contents>
104 </output>
105 <expand macro="logfile-test"/>
106 </test>
107 <test><!-- test with tree input -->
108 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
109 <param name="havedesign" value="no"/>
110 <param name="tree" value="amazon.an.jclass.unique.tre"/>
111 <param name="groups" value="forest,pasture"/>
112 <output name="summary">
113 <assert_contents>
114 <has_text text="TreeNode"/>
115 <has_text text="forest-pasture"/>
116 </assert_contents>
117 </output>
118 <output name="tree_out" md5="a22f90898611e1f4c5d84cfe18dc6ebe"/>
119 <expand macro="logfile-test"/>
120 </test>
121 <test><!-- test with tree input and subset of groups -->
122 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
123 <param name="havedesign" value="no"/>
124 <param name="tree" value="amazon.an.jclass.unique.tre"/>
125 <param name="groups" value="forest"/>
126 <output name="summary">
127 <assert_contents>
128 <has_text text="TreeNode"/>
129 <not_has_text text="forest-pasture"/>
130 </assert_contents>
131 </output>
132 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/>
133 <expand macro="logfile-test"/>
134 </test>
135 </tests>
136 <help>
137 <![CDATA[
138
139 @MOTHUR_OVERVIEW@
140
141 **Command Documenation**
142
143 The indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.
144
145 .. _shared: http://www.mothur.org/wiki/Shared_file
146 .. _relabund: http://www.mothur.org/wiki/Get.relabund
147 .. _indicator: http://www.mothur.org/wiki/Indicator
148
149 v.1.22.0: Updated to Mothur 1.33
150 ]]>
151 </help>
152 <expand macro="citations"/>
153 </tool>