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comparison mothur/tools/mothur/get.oturep.xml @ 2:e990ac8a0f58

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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:39:06 -0400
parents fcc0778f6987
children 5265aa9067e0
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1:fcc0778f6987 2:e990ac8a0f58
1 <tool id="mothur_get_oturep" name="Get.oturep" version="1.16.0" force_history_refresh="True"> 1 <tool id="mothur_get_oturep" name="Get.oturep" version="1.19.0" force_history_refresh="True">
2 <description>Generate a fasta with a representative sequence for each OTU</description> 2 <description>Generate a fasta with a representative sequence for each OTU</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='get.oturep' 5 --cmd='get.oturep'
6 --result='^mothur.\S+\.logfile$:'$logfile 6 --result='^mothur.\S+\.logfile$:'$logfile
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 8 #if $as_datasets.__str__ == "yes":
9 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names' 9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
10 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names'
11 #end if
10 --fasta=$fasta 12 --fasta=$fasta
11 --list=$otu_list 13 --list=$otu_list
12 #if $input.source == 'column': 14 #if $input.source == 'column':
13 --column=$input.dist 15 --column=$input.dist
14 --name=$input.name 16 --name=$input.name
19 #end if 21 #end if
20 #end if 22 #end if
21 #if $label.__str__ != "None" and len($label.__str__) > 0: 23 #if $label.__str__ != "None" and len($label.__str__) > 0:
22 --label='$label' 24 --label='$label'
23 #end if 25 #end if
24 #if $groups.__str__ != "None" and len($groups.__str__) > 0: 26 #if $pick.type == 'yes':
25 --groups=$groups 27 #if $pick.group.__str__ != "None" and len($pick.group.__str__) > 0:
28 --group=$pick.group
29 #end if
30 #if $pick.groups.__str__ != "None" and len($pick.groups.__str__) > 0:
31 --groups=$pick.groups
32 #end if
26 #end if 33 #end if
27 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: 34 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0:
28 --sorted=$sorted 35 --sorted=$sorted
29 #end if 36 #end if
30 $large 37 $large
32 <inputs> 39 <inputs>
33 <!-- get.relabund relabund type should also work --> 40 <!-- get.relabund relabund type should also work -->
34 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> 41 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
35 <param name="otu_list" type="data" format="list" label="list - OTU List"/> 42 <param name="otu_list" type="data" format="list" label="list - OTU List"/>
36 <conditional name="input"> 43 <conditional name="input">
37 <param name="source" type="select" label="Distance Matrix"> 44 <param name="source" type="select" label="Distance Matrix Format">
38 <option value="column">Pairwise Column Distance Matrix</option> 45 <option value="column">Pairwise Column Distance Matrix</option>
39 <option value="phylip">Phylip Distance Matrix</option> 46 <option value="phylip">Phylip Distance Matrix</option>
40 </param> 47 </param>
41 <when value="column"> 48 <when value="column">
42 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> 49 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
43 <param name="name" type="data" format="names" label="name - Sequences Name reference"/> 50 <param name="name" type="data" format="names" label="name - Sequences Name reference"/>
44 </when> 51 </when>
45 <when value="phylip"> 52 <when value="phylip">
46 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> 53 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
47 <param name="name" type="data" format="names" optional="true" label="name - Names"/> 54 <param name="name" type="data" format="names" optional="true" label="name - Names"/>
48 </when> 55 </when>
49 </conditional> 56 </conditional>
50 <param name="group" type="data" format="groups" optional="true" label="group - Group file for the OTU List"/> 57 <conditional name="pick">
51 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> 58 <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
52 <options from_dataset="group"> 59 <option value="no" selected="true">No</option>
53 <column name="name" index="1"/> 60 <option value="yes">Yes</option>
54 <column name="value" index="1"/> 61 </param>
55 </options> 62 <when value="no"/>
56 </param> 63 <when value="yes">
64 <param name="group" type="data" format="groups" label="group - Group file for the OTU List"/>
65 <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true">
66 <options from_dataset="group">
67 <column name="name" index="1"/>
68 <column name="value" index="1"/>
69 <filter type="unique_value" name="unq_grp" column="1" />
70 </options>
71 </param>
72 </when>
73 </conditional> <!-- pick -->
57 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 74 <param name="label" type="select" label="label - OTU Labels" multiple="true">
58 <options from_dataset="otu_list"> 75 <options from_dataset="otu_list">
59 <column name="name" index="0"/> 76 <column name="name" index="0"/>
60 <column name="value" index="0"/> 77 <column name="value" index="0"/>
61 </options> 78 </options>
65 <option value="name">Sequence Name</option> 82 <option value="name">Sequence Name</option>
66 <option value="number">Bin Number</option> 83 <option value="number">Bin Number</option>
67 <option value="size">Bin Size</option> 84 <option value="size">Bin Size</option>
68 <option value="group">Group</option> 85 <option value="group">Group</option>
69 </param> 86 </param>
70
71 <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/> 87 <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/>
88 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/>
72 </inputs> 89 </inputs>
73 <outputs> 90 <outputs>
74 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 91 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
75 </outputs> 92 </outputs>
76 <requirements> 93 <requirements>