Mercurial > repos > iuc > mothur_summary_seqs

annotate summary.seqs.xml @ 11:ece6ab750232 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 20:31:28 +0000
parents 6082f78ea7cb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool profile="16.07" id="mothur_summary_seqs" name="Summary.seqs" version="@WRAPPER_VERSION@.0">
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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
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12 ## create symlinks to input datasets
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13 ln -s '$fasta' fasta.dat &&
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14 ln -s '$name' name.dat &&
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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 $count:
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23 count=count.dat,
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24 #end if
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25 processors='\${GALAXY_SLOTS:-8}'
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26 )'
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27 | sed 's/ //g' ## mothur trips over whitespace
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28 | mothur
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29 | tee mothur.out.log
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30 ]]></command>
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31 <inputs>
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32 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Dataset"/>
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33 <param name="name" type="data" format="mothur.names" label="name - Names" optional="true"/>
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34 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. "/>
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35 <expand macro="param-savelog"/>
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36 </inputs>
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37 <outputs>
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38 <expand macro="logfile-output"/>
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39 <data name="out_summary" format="mothur.summary" from_work_dir="fasta*.summary" label="${tool.name} on ${on_string}: summary"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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44 <output name="out_summary" file="Mock_S280_L001_R1_001_small.trim.contigs.summary" ftype="mothur.summary"/>
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45 <param name="savelog" value="true"/>
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46 <expand macro="logfile-test"/>
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47 </test>
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48 <test><!-- test names input -->
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49 <param name="fasta" value="amazon.unique.fasta"/>
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50 <param name="name" value="amazon.names"/>
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51 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
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52 <param name="savelog" value="true"/>
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53 <expand macro="logfile-test"/>
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54 </test>
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55 <test><!-- test count input -->
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56 <param name="fasta" value="amazon.unique.fasta"/>
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57 <param name="count" value="amazon.count_table"/>
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58 <output name="out_summary" md5="b8a53926f64434291d232d2736da8293" ftype="mothur.summary"/>
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59 <param name="savelog" value="true"/>
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60 <expand macro="logfile-test"/>
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61 </test>
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62 </tests>
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63 <help><![CDATA[
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64
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65 @MOTHUR_OVERVIEW@
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66
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67 **Command Documentation**
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68
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69 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
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70
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71
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72 .. _summary.seqs: https://www.mothur.org/wiki/Summary.seqs
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74 ]]></help>
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75 <expand macro="citations"/>
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76 </tool>