Mercurial > repos > iuc > mothur_count_seqs

comparison count.seqs.xml @ 0:b6f7f17203ad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:56:44 -0400
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-1:000000000000 0:b6f7f17203ad
1 <tool profile="16.07" id="mothur_count_seqs" name="Count.seqs" version="@WRAPPER_VERSION@.0">
2 <description>(aka make.table) counts the number of sequences represented by the representative</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$name" name.dat &&
14 #if $grouping.use == "yes":
15 ln -s "$grouping.group" grouping.group.dat &&
16 #end if
17
18 echo 'count.seqs(
19 name=name.dat,
20 #if $grouping.use == "yes":
21 group=grouping.group.dat,
22 #if $grouping.groups:
23 groups=${ str($grouping.groups).replace(",","-") },
24 #end if
25 #end if
26 large=$large
27 )'
28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur
30 | tee mothur.out.log
31 ]]></command>
32 <inputs>
33 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
34 <conditional name="grouping">
35 <param name="use" type="select" label="Use a Group file to include counts for groups">
36 <option value="no" selected="true">no</option>
37 <option value="yes">yes</option>
38 </param>
39 <when value="yes">
40 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
41 <param name="groups" type="select" label="groups - Groups to display" multiple="true">
42 <help>All groups displayed if none are selected.</help>
43 <options>
44 <filter type="data_meta" ref="group" key="groups"/>
45 </options>
46 </param>
47 </when>
48 <when value="no"/>
49 </conditional>
50 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
51 </inputs>
52 <outputs>
53 <expand macro="logfile-output"/>
54 <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/>
55 </outputs>
56 <tests>
57 <test><!-- test default params -->
58 <param name="name" value="amazon.names"/>
59 <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/>
60 <expand macro="logfile-test"/>
61 </test>
62 <test><!-- test with group file -->
63 <param name="name" value="amazon.names"/>
64 <param name="use" value="yes"/>
65 <param name="group" value="amazon.groups"/>
66 <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/>
67 <expand macro="logfile-test"/>
68 </test>
69 <test> <!-- test with group file and subset of groups -->
70 <param name="name" value="amazon.names"/>
71 <param name="use" value="yes"/>
72 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
73 <param name="groups" value="pasture"/>
74 <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
75 <expand macro="logfile-test"/>
76 </test>
77 <test> <!-- test with group file and multiple groups -->
78 <param name="name" value="amazon.names"/>
79 <param name="use" value="yes"/>
80 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
81 <param name="groups" value="pasture,forest"/>
82 <output name="seq_count" md5="b18c03aee561cd24a36b00ad9b22255a" ftype="mothur.count_table"/>
83 <expand macro="logfile-test"/>
84 </test>
85 </tests>
86 <help>
87 <![CDATA[
88
89 @MOTHUR_OVERVIEW@
90
91 **Command Documentation**
92
93 The count.seqs_ command counts the number of sequences represented by the representative sequence in a name_ file and generates a count_table_. If a group_ file is given, it will also provide the group count breakdown.
94
95 .. _name: https://www.mothur.org/wiki/Name_file
96 .. _group: https://www.mothur.org/wiki/Group_file
97 .. _count.seqs: https://www.mothur.org/wiki/Count.seqs
98 .. _count_table: https://www.mothur.org/wiki/Count_File
99
100 v.1.21.0: Updated to Mothur 1.33
101 ]]>
102 </help>
103 <expand macro="citations"/>
104 </tool>