Mercurial > repos > iuc > mothur_summary_seqs

annotate summary.seqs.xml @ 1:03bc0aa0f9d2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:20:19 -0400
parents a8637d3ac14a
children b7c0b62e024a
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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>
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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="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
0
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12 ## create symlinks to input datasets
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13 ln -s "$fasta" fasta.dat &&
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$name" name.dat &&
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$count" count.dat &&
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16
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17 echo 'summary.seqs(
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18 fasta=fasta.dat,
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19 #if $name:
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20 name=name.dat,
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21 #end if
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22 #if $count:
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23 count=count.dat,
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24 #end if
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25 processors='\${GALAXY_SLOTS:-8}'
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26 )'
a8637d3ac14a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 | sed 's/ //g' ## mothur trips over whitespace
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28 | mothur
1
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29 | tee mothur.out.log
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30 ]]></command>
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31 <inputs>
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32 <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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33 <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
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34 <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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35 </inputs>
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36 <outputs>
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37 <expand macro="logfile-output"/>
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38 <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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43 <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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44 <expand macro="logfile-test"/>
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45 </test>
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46 <test><!-- test names input -->
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47 <param name="fasta" value="amazon.unique.fasta"/>
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48 <param name="name" value="amazon.names"/>
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49 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
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50 <expand macro="logfile-test"/>
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51 </test>
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52 <test><!-- test count input -->
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53 <param name="fasta" value="amazon.unique.fasta"/>
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54 <param name="count" value="amazon.count_table"/>
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55 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
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56 <expand macro="logfile-test"/>
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57 </test>
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58 </tests>
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59 <help>
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60 <![CDATA[
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61
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62 @MOTHUR_OVERVIEW@
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63
1
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64 **Command Documentation**
0
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65
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66 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
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67
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68
1
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69 .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
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70 ]]>
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71 </help>
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72 <expand macro="citations"/>
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73 </tool>