Mercurial > repos > iuc > mothur_count_seqs

comparison count.seqs.xml @ 1:cb4e005b8e8d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:16:37 -0400
parents be91d6962b0c
children 448f43db98c4
comparison
equal deleted inserted replaced
0:be91d6962b0c 1:cb4e005b8e8d
2 <description>(aka make.table) counts the number of sequences represented by the representative</description> 2 <description>(aka make.table) counts the number of sequences represented by the representative</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$name" name.dat && 13 ln -s "$name" name.dat &&
11 #if $grouping.use == "yes": 14 #if $grouping.use == "yes":
12 ln -s "$grouping.group" grouping.group.dat && 15 ln -s "$grouping.group" grouping.group.dat &&
13 #end if 16 #end if
15 echo 'count.seqs( 18 echo 'count.seqs(
16 name=name.dat, 19 name=name.dat,
17 #if $grouping.use == "yes": 20 #if $grouping.use == "yes":
18 group=grouping.group.dat, 21 group=grouping.group.dat,
19 #if $grouping.groups: 22 #if $grouping.groups:
20 groups=$grouping.groups, 23 groups=${ str($grouping.groups).replace(",","-") },
21 #end if 24 #end if
22 #end if 25 #end if
23 large=$large 26 large=$large
24 )' 27 )'
25 | sed 's/ //g' ## mothur trips over whitespace 28 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur 29 | mothur
30 | tee mothur.out.log
27 ]]></command> 31 ]]></command>
28 <inputs> 32 <inputs>
29 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> 33 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
30 <conditional name="grouping"> 34 <conditional name="grouping">
31 <param name="use" type="select" label="Use a Group file to include counts for groups"> 35 <param name="use" type="select" label="Use a Group file to include counts for groups">
68 <param name="group" value="amazon.groups" ftype="mothur.groups"/> 72 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
69 <param name="groups" value="pasture"/> 73 <param name="groups" value="pasture"/>
70 <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/> 74 <output name="seq_count" file="amazon_withgroups_pasture.count_table" ftype="mothur.count_table"/>
71 <expand macro="logfile-test"/> 75 <expand macro="logfile-test"/>
72 </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>
73 </tests> 85 </tests>
74 <help> 86 <help>
75 <![CDATA[ 87 <![CDATA[
76 88
77 @MOTHUR_OVERVIEW@ 89 @MOTHUR_OVERVIEW@
78 90
79 **Command Documenation** 91 **Command Documentation**
80 92
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. 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.
82 94
83 .. _name: http://www.mothur.org/wiki/Name_file 95 .. _name: https://www.mothur.org/wiki/Name_file
84 .. _group: http://www.mothur.org/wiki/Group_file 96 .. _group: https://www.mothur.org/wiki/Group_file
85 .. _count.seqs: http://www.mothur.org/wiki/Count.seqs 97 .. _count.seqs: https://www.mothur.org/wiki/Count.seqs
86 .. _count_table: http://www.mothur.org/wiki/Count_File 98 .. _count_table: https://www.mothur.org/wiki/Count_File
87 99
88 v.1.21.0: Updated to Mothur 1.33 100 v.1.21.0: Updated to Mothur 1.33
89 ]]> 101 ]]>
90 </help> 102 </help>
91 <expand macro="citations"/> 103 <expand macro="citations"/>