Mercurial > repos > iuc > mothur_rarefaction_single

comparison rarefaction.single.xml @ 5:5fa888231577 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:42:08 -0500
parents 3779e72d3525
children b474d518665c
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4:9942d85a53c4 5:5fa888231577
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 14
15 echo 'rarefaction.single( 15 echo 'rarefaction.single(
16 #if $otu.is_of_type("mothur.rabund"): 16 #if $otu.is_of_type("mothur.rabund"):
17 rabund=otu.dat, 17 rabund=otu.dat,
18 #elif $otu.is_of_type("mothur.sabund"): 18 #elif $otu.is_of_type("mothur.sabund"):
19 sabund=otu.dat, 19 sabund=otu.dat,
20 #elif $otu.is_of_type("mothur.shared"): 20 #elif $otu.is_of_type("mothur.shared"):
21 shared=otu.dat, 21 shared=otu.dat,
22 #elif $otu.is_of_type("mothur.list"): 22 #elif $otu.is_of_type("mothur.list"):
23 list=otu.dat, 23 list=otu.dat,
24 #end if 24 #end if
25 #if $label: 25 #if $label:
26 label=${ str($label).replace(",","-") }, 26 label=${ str($label).replace(",","-") },
27 #end if 27 #end if
28 calc=${ str($calc).replace(",","-") }, 28 calc=${ str($calc).replace(",","-") },
29 abund=$abund, 29 abund=$abund,
30 iters=$iters, 30 iters=$iters,
31 freq=$freq, 31 freq=$freq,
32 processors='\${GALAXY_SLOTS:-8}' 32 processors='\${GALAXY_SLOTS:-8}'
33 )' 33 )'
34 | sed 's/ //g' ## mothur trips over whitespace 34 | sed 's/ //g' ## mothur trips over whitespace
35 | mothur 35 | mothur
36 | tee mothur.out.log 36 | tee mothur.out.log
37 37
38 ## rename output from sobs calculator to be consistent with others 38 ## rename output from sobs calculator to be consistent with others
39 #if 'sobs' in str($calc).split(','): 39 #if 'sobs' in str($calc).split(','):
40 && mv otu\.*rarefaction otu.r_sobs 40 && mv otu\.*rarefaction otu.r_sobs
41 #end if 41 #end if
42 ]]></command> 42 ]]></command>
43 <inputs> 43 <inputs>
44 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/> 44 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
45 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 45 <param name="label" type="select" label="label - OTU Labels" multiple="true">
46 <expand macro="labeloptions"/> 46 <expand macro="labeloptions"/>
88 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/> 88 <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
89 </output_collection> 89 </output_collection>
90 <expand macro="logfile-test"/> 90 <expand macro="logfile-test"/>
91 </test> 91 </test>
92 </tests> 92 </tests>
93 <help> 93 <help><![CDATA[
94 <![CDATA[
95 94
96 @MOTHUR_OVERVIEW@ 95 @MOTHUR_OVERVIEW@
97 96
98 **Command Documentation** 97 **Command Documentation**
99 98
100 The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples. For calc parameter choices see: https://www.mothur.org/wiki/Calculators 99 The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
101 100
102 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single 101 .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single
103 ]]> 102
104 </help> 103 ]]></help>
105 <expand macro="citations"/> 104 <expand macro="citations"/>
106 </tool> 105 </tool>