Mercurial > repos > iuc > mothur_summary_qual

annotate summary.qual.xml @ 2:a40036faabe8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:12:40 -0400
parents 41f5224b856b
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41f5224b856b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_summary_qual" name="Summary.qual" version="@WRAPPER_VERSION@.0">
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2 <description>Summarize the quality scores</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[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$qfile' qfile.dat &&
a40036faabe8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$name' name.dat &&
a40036faabe8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$count' count.dat &&
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41f5224b856b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16
2
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17 echo 'summary.qual(
a40036faabe8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 qfile=qfile.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 $count:
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23 ,count=count.dat
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24 #end if
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25 )'
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26 | sed 's/ //g' ## mothur trips over whitespace
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27 | mothur
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28 | tee mothur.out.log
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29 ]]></command>
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30 <inputs>
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31 <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/>
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32 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
41f5224b856b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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34 <expand macro="param-savelog"/>
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35 </inputs>
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36 <outputs>
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37 <expand macro="logfile-output"/>
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38 <data name="out_summary" format="mothur.summary" from_work_dir="qfile*.summary" label="${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="qfile" value="Mock_S280_L001_R1_001_small.trim.contigs.qual"/>
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43 <output name="out_summary" md5="04de7c9d0f3889d5e121db9d9070c935"/>
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44 <param name="savelog" value="true"/>
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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><![CDATA[
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49
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50 @MOTHUR_OVERVIEW@
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51
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52 **Command Documentation**
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53
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54 The summary.qual_ command reads a quality file and an optional name, and summarizes the quality information.
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55
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56 .. _summary.qual: https://www.mothur.org/wiki/Summary.qual
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57
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58 ]]></help>
0
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59 <expand macro="citations"/>
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60 </tool>