Mercurial > repos > iuc > mothur_summary_seqs

annotate summary.seqs.xml @ 0:a8637d3ac14a 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 16:51:58 -0400
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children 03bc0aa0f9d2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a8637d3ac14a 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_summary_seqs" name="Summary.seqs" version="@WRAPPER_VERSION@.0">
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Summarize the quality of sequences</description>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$name" name.dat &&
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$count" count.dat &&
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13
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14 echo 'summary.seqs(
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 fasta=fasta.dat,
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #if $name:
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17 name=name.dat,
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18 #end if
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #if $count:
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 count=count.dat,
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #end if
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 processors='\${GALAXY_SLOTS:-8}'
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 )'
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 | sed 's/ //g' ## mothur trips over whitespace
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 | mothur
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26 ]]></command>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 <inputs>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 </inputs>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <outputs>
a8637d3ac14a 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"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 </outputs>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <tests>
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37 <test>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <expand macro="logfile-test"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 </test>
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42 <test><!-- test names input -->
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43 <param name="fasta" value="amazon.unique.fasta"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <param name="name" value="amazon.names"/>
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45 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <expand macro="logfile-test"/>
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47 </test>
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48 <test><!-- test count input -->
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49 <param name="fasta" value="amazon.unique.fasta"/>
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50 <param name="count" value="amazon.count_table"/>
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51 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
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52 <expand macro="logfile-test"/>
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57
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58 @MOTHUR_OVERVIEW@
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59
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60 **Command Documenation**
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61
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62 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
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63
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64
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65 .. _summary.seqs: http://www.mothur.org/wiki/Summary.seqs
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66 ]]>
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67 </help>
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68 <expand macro="citations"/>
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69 </tool>