Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/make.fastq.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
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children | ee59e5cff3ba |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_make_fastq" name="Make.fastq" version="1.19.0"> | |
2 <description>Convert fasta and quality to fastq</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='fastq.info' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq | |
7 --outputdir='$logfile.extra_files_path' | |
8 --fasta=$fasta | |
9 --qfile=$qfile | |
10 </command> | |
11 <inputs> | |
12 <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> | |
13 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> | |
14 </inputs> | |
15 <outputs> | |
16 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
17 <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq"/> | |
18 </outputs> | |
19 <requirements> | |
20 <requirement type="binary">mothur</requirement> | |
21 </requirements> | |
22 <tests> | |
23 </tests> | |
24 <help> | |
25 **Mothur Overview** | |
26 | |
27 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
28 in the Department of Microbiology and Immunology at The University of Michigan, | |
29 provides bioinformatics for the microbial ecology community. | |
30 | |
31 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
32 | |
33 **Command Documenation** | |
34 | |
35 The fastq.info_ command reads a fasta file and quality file and creates a fastq. | |
36 | |
37 | |
38 .. _fastq.info: http://www.mothur.org/wiki/Make.fastq | |
39 | |
40 </help> | |
41 </tool> |