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comparison indicator.xml @ 3:c6524e1efe12 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:10:48 -0400
parents 5d1f9418ff72
children 0232e2fe594c
comparison
equal deleted inserted replaced
2:5d1f9418ff72 3:c6524e1efe12
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$otu" otu.dat && 13 ln -s '$otu' otu.dat &&
14 #if $withdesign.tree: 14 #if $withdesign.tree:
15 ln -s "$withdesign.tree" withdesign.tree.dat && 15 ln -s '$withdesign.tree' withdesign.tree.dat &&
16 #end if 16 #end if
17 #if $withdesign.havedesign == "yes": 17 #if $withdesign.havedesign == "yes":
18 ln -s "$withdesign.design" withdesign.design.dat && 18 ln -s '$withdesign.design' withdesign.design.dat &&
19 #end if 19 #end if
20 20
21 echo 'indicator( 21 echo 'indicator(
22 #if $withdesign.tree: 22 #if $withdesign.tree:
23 tree=withdesign.tree.dat, 23 tree=withdesign.tree.dat,
24 #end if 24 #end if
25 #if $otu.is_of_type("mothur.relabund"): 25 #if $otu.is_of_type("mothur.relabund"):
26 relabund=otu.dat, 26 relabund=otu.dat,
27 #elif $otu.is_of_type("mothur.shared"): 27 #elif $otu.is_of_type("mothur.shared"):
28 shared=otu.dat, 28 shared=otu.dat,
29 #end if 29 #end if
30 #if $label: 30 #if $label:
31 label=${ str($label).replace(",","-") }, 31 label=${ str($label).replace(",","-") },
32 #end if 32 #end if
33 #if $withdesign.groups: 33 #if $withdesign.groups:
34 groups=${ str($withdesign.groups).replace(",","-") }, 34 groups=${ str($withdesign.groups).replace(",","-") },
35 #end if 35 #end if
36 #if $withdesign.havedesign == "yes": 36 #if $withdesign.havedesign == "yes":
37 design=withdesign.design.dat, 37 design=withdesign.design.dat,
38 #end if 38 #end if
39 processors='\${GALAXY_SLOTS:-8}' 39 processors='\${GALAXY_SLOTS:-8}'
40 )' 40 )'
41 | sed 's/ //g' ## mothur trips over whitespace 41 | sed 's/ //g' ## mothur trips over whitespace
42 | mothur 42 | mothur
43 | tee mothur.out.log 43 | tee mothur.out.log
44 ]]></command> 44 ]]></command>
45 <inputs> 45 <inputs>
46 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/> 46 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/>
47 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels"> 47 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels">
48 <expand macro="labeloptions"/> 48 <expand macro="labeloptions"/>
68 <filter type="data_meta" ref="otu" key="groups"/> 68 <filter type="data_meta" ref="otu" key="groups"/>
69 </options> 69 </options>
70 </param> 70 </param>
71 </when> 71 </when>
72 </conditional> 72 </conditional>
73 <expand macro="param-savelog"/>
73 </inputs> 74 </inputs>
74 <outputs> 75 <outputs>
75 <expand macro="logfile-output"/> 76 <expand macro="logfile-output"/>
76 <data name="tree_out" format="mothur.tre" from_work_dir="withdesign.tree*.tre" label="${tool.name} on ${on_string}: indicator.tre"> 77 <data name="tree_out" format="mothur.tre" from_work_dir="withdesign.tree*.tre" label="${tool.name} on ${on_string}: indicator.tre">
77 <filter>tree</filter> 78 <filter>tree</filter>
90 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/> 91 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
91 <has_text text="forest"/> 92 <has_text text="forest"/>
92 <has_text text="pasture"/> 93 <has_text text="pasture"/>
93 </assert_contents> 94 </assert_contents>
94 </output> 95 </output>
96 <param name="savelog" value="true"/>
95 <expand macro="logfile-test"/> 97 <expand macro="logfile-test"/>
96 </test> 98 </test>
97 <test><!-- test with design input and subset of groups--> 99 <test><!-- test with design input and subset of groups-->
98 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 100 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
99 <param name="havedesign" value="yes"/> 101 <param name="havedesign" value="yes"/>
104 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/> 106 <has_line_matching expression="^OTU\tIndicator_Groups\tIndicator_Value\tpValue$"/>
105 <has_text text="forest"/> 107 <has_text text="forest"/>
106 <not_has_text text="pasture"/> 108 <not_has_text text="pasture"/>
107 </assert_contents> 109 </assert_contents>
108 </output> 110 </output>
111 <param name="savelog" value="true"/>
109 <expand macro="logfile-test"/> 112 <expand macro="logfile-test"/>
110 </test> 113 </test>
111 <test><!-- test with tree input --> 114 <test><!-- test with tree input -->
112 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 115 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
113 <param name="havedesign" value="no"/> 116 <param name="havedesign" value="no"/>
118 <has_text text="TreeNode"/> 121 <has_text text="TreeNode"/>
119 <has_text text="forest-pasture"/> 122 <has_text text="forest-pasture"/>
120 </assert_contents> 123 </assert_contents>
121 </output> 124 </output>
122 <output name="tree_out" md5="a22f90898611e1f4c5d84cfe18dc6ebe"/> 125 <output name="tree_out" md5="a22f90898611e1f4c5d84cfe18dc6ebe"/>
126 <param name="savelog" value="true"/>
123 <expand macro="logfile-test"/> 127 <expand macro="logfile-test"/>
124 </test> 128 </test>
125 <test><!-- test with tree input and subset of groups --> 129 <test><!-- test with tree input and subset of groups -->
126 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> 130 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
127 <param name="havedesign" value="no"/> 131 <param name="havedesign" value="no"/>
132 <has_text text="TreeNode"/> 136 <has_text text="TreeNode"/>
133 <not_has_text text="forest-pasture"/> 137 <not_has_text text="forest-pasture"/>
134 </assert_contents> 138 </assert_contents>
135 </output> 139 </output>
136 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/> 140 <output name="tree_out" md5="756bfd16311e141a099cfe96db458d83"/>
141 <param name="savelog" value="true"/>
137 <expand macro="logfile-test"/> 142 <expand macro="logfile-test"/>
138 </test> 143 </test>
139 </tests> 144 </tests>
140 <help> 145 <help><![CDATA[
141 <![CDATA[
142 146
143 @MOTHUR_OVERVIEW@ 147 @MOTHUR_OVERVIEW@
144 148
145 **Command Documentation** 149 **Command Documentation**
146 150
149 .. _shared: https://www.mothur.org/wiki/Shared_file 153 .. _shared: https://www.mothur.org/wiki/Shared_file
150 .. _relabund: https://www.mothur.org/wiki/Get.relabund 154 .. _relabund: https://www.mothur.org/wiki/Get.relabund
151 .. _indicator: https://www.mothur.org/wiki/Indicator 155 .. _indicator: https://www.mothur.org/wiki/Indicator
152 156
153 v.1.22.0: Updated to Mothur 1.33 157 v.1.22.0: Updated to Mothur 1.33
154 ]]> 158
155 </help> 159 ]]></help>
156 <expand macro="citations"/> 160 <expand macro="citations"/>
157 </tool> 161 </tool>