Mercurial > repos > iuc > mothur_shhh_seqs

annotate shhh.seqs.xml @ 0:55a2994f3f3e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:50:16 -0400
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children 48c4a9ef85e6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_shhh_seqs" name="Shhh.seqs" version="@WRAPPER_VERSION@.0">
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Denoise program (Quince SeqNoise)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
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10 ln -s "$fasta" fasta.dat &&
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$name" name.dat &&
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$group" group.dat &&
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 echo 'shhh.seqs(
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 fasta=fasta.dat,
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 name=name.dat,
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #if $group:
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18 group=group.dat,
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #end if
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 sigma=$sigma,
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 processors='\${GALAXY_SLOTS:-8}'
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 )'
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23 | sed 's/ //g' ## mothur trips over whitespace
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 | mothur
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25 ]]></command>
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26 <inputs>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 </inputs>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <outputs>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <expand macro="logfile-output"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <data name="shhh_map" format="txt" from_work_dir="fasta*.shhh_seqs.map" label="${tool.name} on ${on_string}: shhh.map"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 </outputs>
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38 <tests>
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39 <test>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/>
55a2994f3f3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <expand macro="logfile-test"/>
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46 </test>
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47 </tests>
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48 <help>
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49 <![CDATA[
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50
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51 @MOTHUR_OVERVIEW@
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52
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53 **Command Documenation**
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54
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55 The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise. Schloss prefers pre.cluster for this operation.
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56
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57 .. _shhh.seqs: http://www.mothur.org/wiki/Shhh.seqs
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58
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59 ]]>
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60 </help>
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61 <expand macro="citations"/>
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62 </tool>