Mercurial > repos > iuc > mothur_phylo_diversity

comparison phylo.diversity.xml @ 2:292c7c4d2789 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 22:24:23 -0400
parents 917aa3b39ccd
children e398beade8e7
comparison
equal deleted inserted replaced
1:a5c241267a5f 2:292c7c4d2789
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 "$tree" tree.dat && 13 ln -s '$tree' tree.dat &&
14 ln -s "$name" name.dat && 14 ln -s '$name' name.dat &&
15 ln -s "$count" count.dat && 15 ln -s '$count' count.dat &&
16 #if $grouping.use == "yes": 16 #if $grouping.use == "yes":
17 ln -s "$grouping.group" grouping.group.dat && 17 ln -s '$grouping.group' grouping.group.dat &&
18 #end if
19
20 echo 'phylo.diversity(
21 tree=tree.dat,
22 #if $grouping.use == "yes":
23 group=grouping.group.dat,
24 #if $grouping.groups:
25 groups=${ str($grouping.groups).replace(",","-") },
18 #end if 26 #end if
19 27 #end if
20 echo 'phylo.diversity( 28 #if $name:
21 tree=tree.dat, 29 name=name.dat,
22 #if $grouping.use == "yes": 30 #end if
23 group=grouping.group.dat, 31 iters=$iters,
24 #if $grouping.groups: 32 freq=$freq,
25 groups=${ str($grouping.groups).replace(",","-") }, 33 scale=$scale,
26 #end if 34 collect=$collect,
27 #end if 35 rarefy=$rarefy,
28 #if $name: 36 summary=$summary,
29 name=name.dat, 37 #if $count:
30 #end if 38 count=count.dat,
31 iters=$iters, 39 #end if
32 freq=$freq, 40 processors='\${GALAXY_SLOTS:-8}'
33 scale=$scale, 41 )'
34 collect=$collect, 42 | sed 's/ //g' ## mothur trips over whitespace
35 rarefy=$rarefy, 43 | mothur
36 summary=$summary, 44 | tee mothur.out.log
37 #if $count:
38 count=count.dat,
39 #end if
40 processors='\${GALAXY_SLOTS:-8}'
41 )'
42 | sed 's/ //g' ## mothur trips over whitespace
43 | mothur
44 | tee mothur.out.log
45 ]]></command> 45 ]]></command>
46 <inputs> 46 <inputs>
47 <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/> 47 <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
48 <conditional name="grouping"> 48 <conditional name="grouping">
49 <param name="use" type="select" label="Analyze by group using a Group file"> 49 <param name="use" type="select" label="Analyze by group using a Group file">
67 <param name="scale" type="boolean" truevalue="true" falsevalue="false" checked="false" label="scale - Scale output to the number of sequences sampled"/> 67 <param name="scale" type="boolean" truevalue="true" falsevalue="false" checked="false" label="scale - Scale output to the number of sequences sampled"/>
68 <param name="rarefy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="rarefy - Calculate the rarefaction data"/> 68 <param name="rarefy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="rarefy - Calculate the rarefaction data"/>
69 <param name="summary" type="boolean" truevalue="true" falsevalue="false" checked="true" label="summary - Generate a summary file"/> 69 <param name="summary" type="boolean" truevalue="true" falsevalue="false" checked="true" label="summary - Generate a summary file"/>
70 <param name="collect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="collect - Create a collectors curve"/> 70 <param name="collect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="collect - Create a collectors curve"/>
71 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> 71 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
72 <expand macro="param-savelog"/>
72 </inputs> 73 </inputs>
73 <outputs> 74 <outputs>
74 <expand macro="logfile-output"/> 75 <expand macro="logfile-output"/>
75 <data name="summary_out" format="tabular" from_work_dir="tree*.phylodiv.summary" label="${tool.name} on ${on_string}: summary"> 76 <data name="summary_out" format="tabular" from_work_dir="tree*.phylodiv.summary" label="${tool.name} on ${on_string}: summary">
76 <filter>summary</filter> 77 <filter>summary</filter>
85 <tests> 86 <tests>
86 <test><!-- test with tree file only --> 87 <test><!-- test with tree file only -->
87 <param name="tree" value="treetest.tre" ftype="mothur.tre"/> 88 <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
88 <param name="use" value="no"/> 89 <param name="use" value="no"/>
89 <output name="summary_out" md5="a9feb4031094b555baf62e0165dd3637" ftype="tabular"/> 90 <output name="summary_out" md5="a9feb4031094b555baf62e0165dd3637" ftype="tabular"/>
91 <param name="savelog" value="true"/>
90 <expand macro="logfile-test"/> 92 <expand macro="logfile-test"/>
91 </test> 93 </test>
92 <test><!-- test with tree file and group file and all outputs --> 94 <test><!-- test with tree file and group file and all outputs -->
93 <param name="tree" value="treetest.tre" ftype="mothur.tre"/> 95 <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
94 <param name="use" value="yes"/> 96 <param name="use" value="yes"/>
109 <has_text text="numSampled"/> 111 <has_text text="numSampled"/>
110 <has_text text="orange"/> 112 <has_text text="orange"/>
111 <has_text text="green"/> 113 <has_text text="green"/>
112 </assert_contents> 114 </assert_contents>
113 </output> 115 </output>
116 <param name="savelog" value="true"/>
114 <expand macro="logfile-test"/> 117 <expand macro="logfile-test"/>
115 </test> 118 </test>
116 </tests> 119 </tests>
117 <help> 120 <help><![CDATA[
118 <![CDATA[
119 121
120 @MOTHUR_OVERVIEW@ 122 @MOTHUR_OVERVIEW@
121 123
122 124
123 **Command Documentation** 125 **Command Documentation**
126 128
127 .. _phylo.diversity: https://www.mothur.org/wiki/Phylo.diversity 129 .. _phylo.diversity: https://www.mothur.org/wiki/Phylo.diversity
128 130
129 v.1.21.0: Updated to Mothur 1.33, added count parameter 131 v.1.21.0: Updated to Mothur 1.33, added count parameter
130 132
131 ]]> 133 ]]></help>
132 </help>
133 <expand macro="citations"/> 134 <expand macro="citations"/>
134 </tool> 135 </tool>