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annotate obisort.xml @ 1:fe736681bbd8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
author iuc
date Fri, 12 Oct 2018 06:18:47 -0400
parents bfec1056dceb
children 25393415c6c9
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fe736681bbd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit b3426aed6615742d96dfb8f7346a9e0d4e391a99
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1 <tool id="obi_sort" name="obisort" version="@TOOL_VERSION@">
0
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2 <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</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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9 <command>
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11 <![CDATA[
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12 obisort
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13 -k '$key'
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14 ${reverse}
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15 '$input' > '$output'
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16 ]]>
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18 </command>
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20 <inputs>
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21 <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
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22 <param name="key" type="text" label="key" />
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23 <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
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24 <param name="out_format" type="select" label="Output data type">
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25 <option value="fasta">fasta</option>
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26 <option value="fastq">fastq</option>
bfec1056dceb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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27 </param>
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29 </inputs>
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30 <outputs>
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31 <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" >
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32 <change_format>
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33 <when input="out_format" value="fasta" format="fasta" />
bfec1056dceb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
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34 </change_format>
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35 </data>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" value="output_obiclean_advanced.fasta" />
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40 <param name="key" value="count"/>
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41 <param name="reverse" value="False"/>
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42 <param name="out_format" value="fasta"/>
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43 <output name="output" file="output_obisort.fasta" ftype="fasta"/>
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44 </test>
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45 <test>
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46 <param name="input" value="output_obiclean_advanced.fasta" />
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47 <param name="key" value="count"/>
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48 <param name="reverse" value="True"/>
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49 <param name="out_format" value="fastq"/>
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50 <output name="output" file="output_obisort.fastq" ftype="fastq"/>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54
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55 .. class:: infomark
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56
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57 **What it does**
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58
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59 obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric.
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61 @OBITOOLS_LINK@
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63 ]]>
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65 </help>
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66 <expand macro="citation" />
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67 </tool>