Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/rarefaction.shared.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
parents | bfbaf823be4c |
children | 95d75b35e4d2 |
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26:5c77423823cb | 27:49058b1f8d3f |
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1 <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.20.0"> | 1 <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.26.0" force_history_refresh="True"> |
2 <description>Generate inter-sample rarefaction curves for OTUs</description> | 2 <description>Generate inter-sample rarefaction curves for OTUs</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='rarefaction.shared' | 5 --cmd='rarefaction.shared' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction |
10 --label='$label' | 10 --label='$label' |
11 #end if | 11 #end if |
12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: | 12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
13 --groups=$groups | 13 --groups=$groups |
14 #end if | 14 #end if |
15 #if $design.use: | |
16 --design=$design.design | |
17 #if $design.sets.__str__ != '': | |
18 --sets='$design.sets' | |
19 #end if | |
20 #end if | |
15 #if int($iters.__str__) > 0: | 21 #if int($iters.__str__) > 0: |
16 --iters=$iters | 22 --iters=$iters |
17 #end if | 23 #end if |
18 $jumble | 24 $jumble |
19 #if $calc.__str__ != "None" and len($calc.__str__) > 0: | 25 #if $calc.__str__ != "None" and len($calc.__str__) > 0: |
20 --calc='$calc' | 26 --calc='$calc' |
27 #end if | |
28 #if $subsample.use.__str__ == 'yes': | |
29 #if $subsample.subsample.__str__ != '': | |
30 --subsample=$subsample.subsample | |
31 #else | |
32 --subsample=T | |
33 #end if | |
34 #if $subsample.subsampleiters.__str__ != '': | |
35 --subsampleiters=$subsample.subsampleiters | |
36 #end if | |
37 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' | |
38 --new_datasets='^\S+?\.ave-std\.((unique|[0-9.]*)(\..*?)+\.shared\.rarefaction)$:tabular' | |
21 #end if | 39 #end if |
22 </command> | 40 </command> |
23 <inputs> | 41 <inputs> |
24 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> | 42 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/> |
25 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | 43 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
29 </param> | 47 </param> |
30 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> | 48 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true"> |
31 <help>All groups will be analyzed by default if none are selected</help> | 49 <help>All groups will be analyzed by default if none are selected</help> |
32 <options> | 50 <options> |
33 <filter type="data_meta" ref="otu" key="groups" /> | 51 <filter type="data_meta" ref="otu" key="groups" /> |
52 <!-- | |
34 <filter type="add_value" name="all" value="all" /> | 53 <filter type="add_value" name="all" value="all" /> |
54 --> | |
35 </options> | 55 </options> |
36 </param> | 56 </param> |
57 <conditional name="design"> | |
58 <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label=" run on a per set basis using a design file"/> | |
59 <when value="yes"> | |
60 <param name="design" type="data" format="design" label="design - assigns groups to sets" | |
61 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> | |
62 <param name="sets" type="select" label="sets - group sets to analyze" multiple="true"> | |
63 <options> | |
64 <filter type="data_meta" ref="design" key="groups" /> | |
65 </options> | |
66 </param> | |
67 </when> | |
68 <when value="no"/> | |
69 </conditional> | |
70 | |
37 <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/> | 71 <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/> |
38 <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/> | 72 <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/> |
39 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> | 73 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> |
40 <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option> | 74 <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option> |
41 <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option> | 75 <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option> |
42 </param> | 76 </param> |
77 <conditional name="subsample"> | |
78 <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample rarefactions"/> | |
79 <when value="yes"> | |
80 <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" | |
81 help="Leave blank to use the size of your smallest group"/> | |
82 <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/> | |
83 </when> | |
84 <when value="no"/> | |
85 </conditional> | |
86 | |
43 </inputs> | 87 </inputs> |
44 <outputs> | 88 <outputs> |
45 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 89 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
46 <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" /> | 90 <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" /> |
47 </outputs> | 91 </outputs> |
48 <requirements> | 92 <requirements> |
49 <requirement type="binary">mothur</requirement> | 93 <requirement type="package" version="1.27">mothur</requirement> |
50 </requirements> | 94 </requirements> |
51 <tests> | 95 <tests> |
52 </tests> | 96 </tests> |
53 <help> | 97 <help> |
54 **Mothur Overview** | 98 **Mothur Overview** |