Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/sffinfo.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 |
parents | fcc0778f6987 |
children | a6189f58fedb |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_sffinfo" name="Sffinfo" version="1.19.0"> |
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2 <description>Summarize the quality of sequences</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='sffinfo' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile,'^\S+\.sff\.txt$:'$out_sfftxt,'^\S+\.flow$:'$out_flow |
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7 --outputdir='$logfile.extra_files_path' |
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8 --sff=$sff |
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9 $fasta |
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10 $qfile |
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11 $sfftxt |
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12 $flow |
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13 $trim |
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14 #if $accnos.__str__ != 'None' and len($accnos.__str__) > 0: |
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15 --accnos=$accnos |
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16 #end if |
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17 </command> |
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18 <inputs> |
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19 <param name="sff" type="data" format="sff" label="sff - Sff data"/> |
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20 <!-- |
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21 <repeat name="more" title="Additional "> |
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22 <param name="sff" type="data" format="sff" label="sff - Sff data"/> |
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23 </repeat> |
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24 --> |
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25 <!-- |
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26 <param name="datasets" type="select" display="checkboxes" multiple="True" label="datasets - Choose output files for your history" help="Selected outputs will be listed as datasets in your history"> |
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27 <option value="fasta">fasta</option> |
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28 <option value="qfile">qfile</option> |
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29 <option value="sfftxt">sfftxt</option> |
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30 <option value="flow">flow</option> |
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31 </param> |
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32 --> |
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33 <param name="fasta" type="boolean" truevalue="" falsevalue="--fasta=false" checked="true" label="fasta - Add fasta to your history" /> |
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34 <param name="qfile" type="boolean" truevalue="" falsevalue="--qfile=false" checked="true" label="qfile - Add qfile to your history" /> |
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35 <param name="sfftxt" type="boolean" truevalue="--sfftxt=true" falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history" /> |
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36 <param name="flow" type="boolean" truevalue="--flow=true" falsevalue="" checked="false" label="flow - Add flow to your history" /> |
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37 <param name="trim" type="boolean" truevalue="" falsevalue="--trim=false" checked="true" label="trim - Trim sequences and quality scores" /> |
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38 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Limit output to named Accessions"/> |
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39 </inputs> |
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40 <outputs> |
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41 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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42 <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta"> |
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43 <filter>fasta == True</filter> |
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44 </data> |
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45 <data format="qual454" name="out_qfile" label="${tool.name} on ${on_string}: qual"> |
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46 <filter>qfile == True</filter> |
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47 </data> |
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48 <data format="txt" name="out_sfftxt" label="${tool.name} on ${on_string}: sff.txt"> |
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49 <filter>sfftxt == True</filter> |
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50 </data> |
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51 <data format="txt" name="out_flow" label="${tool.name} on ${on_string}: flowgram"> |
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52 <filter>flow == True</filter> |
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53 </data> |
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54 </outputs> |
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55 <requirements> |
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56 <requirement type="binary">mothur</requirement> |
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57 </requirements> |
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58 <tests> |
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59 </tests> |
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60 <help> |
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61 **Mothur Overview** |
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62 |
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63 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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64 in the Department of Microbiology and Immunology at The University of Michigan, |
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65 provides bioinformatics for the microbial ecology community. |
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66 |
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67 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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68 |
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69 **Command Documenation** |
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70 |
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71 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. |
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72 |
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73 |
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74 .. _sffinfo: http://www.mothur.org/wiki/Sffinfo |
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75 |
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76 </help> |
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77 </tool> |