Mercurial > repos > iuc > mothur_get_seqs

comparison get.seqs.xml @ 1:fa04cbc39523 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 05:13:13 -0400
parents d54a9887df4a
children ef6de2793ab6
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0:d54a9887df4a 1:fa04cbc39523
2 <description>Picks sequences by name</description> 2 <description>Picks sequences by name</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 "$accnos" accnos.dat && 13 ln -s "$accnos" accnos.dat &&
11 ln -s "$fasta_in" fasta_in.dat && 14 ln -s "$fasta_in" fasta_in.dat &&
12 ln -s "$fastq_in" fastq_in.dat && 15 ln -s "$fastq_in" fastq_in.dat &&
13 ln -s "$count_in" count_in.dat && 16 ln -s "$count_in" count_in.dat &&
49 #end if 52 #end if
50 dups=$dups 53 dups=$dups
51 )' 54 )'
52 | sed 's/ //g' ## mothur trips over whitespace 55 | sed 's/ //g' ## mothur trips over whitespace
53 | mothur 56 | mothur
57 | tee mothur.out.log
54 ]]></command> 58 ]]></command>
55 <inputs> 59 <inputs>
56 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/> 60 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/>
57 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> 61 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
58 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> 62 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
129 <help> 133 <help>
130 <![CDATA[ 134 <![CDATA[
131 135
132 @MOTHUR_OVERVIEW@ 136 @MOTHUR_OVERVIEW@
133 137
134 **Command Documenation** 138 **Command Documentation**
135 139
136 The get.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection. 140 The get.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
137 141
138 .. _name: http://www.mothur.org/wiki/Name_file 142 .. _name: https://www.mothur.org/wiki/Name_file
139 .. _group: http://www.mothur.org/wiki/Group_file 143 .. _group: https://www.mothur.org/wiki/Group_file
140 .. _list: http://www.mothur.org/wiki/List_file 144 .. _list: https://www.mothur.org/wiki/List_file
141 .. _align.report: http://www.mothur.org/wiki/Align.seqs 145 .. _align.report: https://www.mothur.org/wiki/Align.seqs
142 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline 146 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
143 .. _list.seqs: http://www.mothur.org/wiki/list.seqs 147 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
144 .. _get.seqs: http://www.mothur.org/wiki/Get.seqs 148 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs
145 149
146 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params 150 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
147 ]]> 151 ]]>
148 </help> 152 </help>
149 <expand macro="citations"/> 153 <expand macro="citations"/>