Mercurial > repos > iuc > mothur_count_seqs

comparison count.seqs.xml @ 0:be91d6962b0c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:28:37 -0400
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-1:000000000000 0:be91d6962b0c
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="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$name" name.dat &&
11 #if $grouping.use == "yes":
12 ln -s "$grouping.group" grouping.group.dat &&
13 #end if
14
15 echo 'count.seqs(
16 name=name.dat,
17 #if $grouping.use == "yes":
18 group=grouping.group.dat,
19 #if $grouping.groups:
20 groups=$grouping.groups,
21 #end if
22 #end if
23 large=$large
24 )'
25 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur
27 ]]></command>
28 <inputs>
29 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
30 <conditional name="grouping">
31 <param name="use" type="select" label="Use a Group file to include counts for groups">
32 <option value="no" selected="true">no</option>
33 <option value="yes">yes</option>
34 </param>
35 <when value="yes">
36 <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
37 <param name="groups" type="select" label="groups - Groups to display" multiple="true">
38 <help>All groups displayed if none are selected.</help>
39 <options>
40 <filter type="data_meta" ref="group" key="groups"/>
41 </options>
42 </param>
43 </when>
44 <when value="no"/>
45 </conditional>
46 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/>
47 </inputs>
48 <outputs>
49 <expand macro="logfile-output"/>
50 <data name="seq_count" format="mothur.count_table" from_work_dir="name*.count_table" label="${tool.name} on ${on_string}: count_table"/>
51 </outputs>
52 <tests>
53 <test><!-- test default params -->
54 <param name="name" value="amazon.names"/>
55 <output name="seq_count" file="amazon.count_table" ftype="mothur.count_table"/>
56 <expand macro="logfile-test"/>
57 </test>
58 <test><!-- test with group file -->
59 <param name="name" value="amazon.names"/>
60 <param name="use" value="yes"/>
61 <param name="group" value="amazon.groups"/>
62 <output name="seq_count" file="amazon_withgroups.count_table" ftype="mothur.count_table"/>
63 <expand macro="logfile-test"/>
64 </test>
65 <test> <!-- test with group file and subset of groups -->
66 <param name="name" value="amazon.names"/>
67 <param name="use" value="yes"/>
68 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
69 <param name="groups" value="pasture"/>
70 <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
71 <expand macro="logfile-test"/>
72 </test>
73 </tests>
74 <help>
75 <![CDATA[
76
77 @MOTHUR_OVERVIEW@
78
79 **Command Documenation**
80
81 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.
82
83 .. _name: http://www.mothur.org/wiki/Name_file
84 .. _group: http://www.mothur.org/wiki/Group_file
85 .. _count.seqs: http://www.mothur.org/wiki/Count.seqs
86 .. _count_table: http://www.mothur.org/wiki/Count_File
87
88 v.1.21.0: Updated to Mothur 1.33
89 ]]>
90 </help>
91 <expand macro="citations"/>
92 </tool>