Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/fastq.info.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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1 <tool id="mothur_fastq_info" name="Fastq.info" version="1.24.0"> |
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2 <description>Convert fastq to fasta and quality</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='fastq.info' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fastq=$fastq |
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9 </command> |
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10 <inputs> |
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11 <param name="fastq" type="data" format="fastq" label="fastq - Fastq Sequence file"/> |
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12 <param name="fasta" type="boolean" truevalue="" falsevalue="--fasta=false" checked="true" label="fasta - Add fasta to your history" /> |
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13 <param name="qfile" type="boolean" truevalue="" falsevalue="--qfile=false" checked="true" label="qfile - Add qfile to your history" /> |
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14 </inputs> |
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15 <outputs> |
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16 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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17 <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta"> |
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18 <filter>fasta == True</filter> |
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19 </data> |
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20 <data format="qual454" name="out_qfile" label="${tool.name} on ${on_string}: qual"> |
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21 <filter>qfile == True</filter> |
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22 </data> |
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23 </outputs> |
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24 <requirements> |
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25 <requirement type="package" version="1.27">mothur</requirement> |
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26 </requirements> |
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27 <tests> |
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28 </tests> |
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29 <help> |
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30 **Mothur Overview** |
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31 |
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32 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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33 in the Department of Microbiology and Immunology at The University of Michigan, |
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34 provides bioinformatics for the microbial ecology community. |
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35 |
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36 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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37 |
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38 **Command Documenation** |
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39 |
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40 The fastq.info_ command reads a fastq file and creates a fasta and quality file. |
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41 |
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42 |
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43 .. _fastq.info: http://www.mothur.org/wiki/Fastq.info |
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44 |
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45 </help> |
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46 </tool> |