Mercurial > repos > iuc > mothur_indicator
comparison indicator.xml @ 3:c6524e1efe12 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
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date | Tue, 20 Mar 2018 22:10:48 -0400 |
parents | 5d1f9418ff72 |
children | 0232e2fe594c |
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2:5d1f9418ff72 | 3:c6524e1efe12 |
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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> |