Mercurial > repos > iuc > mothur_make_fastq

comparison make.fastq.xml @ 1:61b2c4a74b35 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 18:16:15 -0400
parents 10e56de9ad1a
children a17148e8865a
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0:10e56de9ad1a 1:61b2c4a74b35
2 <description>Convert fasta and quality to fastq</description> 2 <description>Convert fasta and quality to fastq</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 "$fasta" fasta.dat && 13 ln -s "$fasta" fasta.dat &&
11 ln -s "$qfile" qfile.dat && 14 ln -s "$qfile" qfile.dat &&
12 15
13 echo 'make.fastq( 16 echo 'make.fastq(
17 ,format=${chooseformat.format} 20 ,format=${chooseformat.format}
18 #end if 21 #end if
19 )' 22 )'
20 | sed 's/ //g' ## mothur trips over whitespace 23 | sed 's/ //g' ## mothur trips over whitespace
21 | mothur 24 | mothur
25 | tee mothur.out.log
22 ]]></command> 26 ]]></command>
23 <inputs> 27 <inputs>
24 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> 28 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/>
25 <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/> 29 <param name="qfile" type="data" format="qual454,qualillumina,qualsolid,qual" label="qfile - Sequence Quality file"/>
26 <conditional name="chooseformat"> 30 <conditional name="chooseformat">
70 <help> 74 <help>
71 <![CDATA[ 75 <![CDATA[
72 76
73 @MOTHUR_OVERVIEW@ 77 @MOTHUR_OVERVIEW@
74 78
75 **Command Documenation** 79 **Command Documentation**
76 80
77 The fastq.info_ command reads a fasta file and quality file and creates a fastq. 81 The fastq.info_ command reads a fasta file and quality file and creates a fastq.
78 82
79 83
80 .. _fastq.info: http://www.mothur.org/wiki/Make.fastq 84 .. _fastq.info: https://www.mothur.org/wiki/Make.fastq
81 ]]> 85 ]]>
82 </help> 86 </help>
83 <expand macro="citations"/> 87 <expand macro="citations"/>
84 </tool> 88 </tool>