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annotate tools/mothur/split.groups.xml @ 0:ee4fee239fe7 draft default tip

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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool profile="16.07" id="mothur_split_groups" name="Split.groups" version="@WRAPPER_VERSION@.0">
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2 <description>Generates a fasta file for each group</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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'split.groups(
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10 #if $name:
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11 name=$name,
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12 #end if
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13 #if $groups:
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14 groups=${ str($groups).replace(",","-") },
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15 #end if
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16 #if $count:
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17 count=$count,
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18 #end if
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19 fasta=$fasta,
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20 group=$group
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21 )'
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22 | sed 's/ //g' ## mothur trips over whitespace
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23 | mothur &&
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24
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25 ## move output files to correct destination
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26 prefix="$fasta" &&
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27 mv mothur.*.logfile "$logfile" &&
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28 mv \${prefix%.dat}*.fasta .
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29 ]]></command>
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30 <inputs>
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31 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
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32 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
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33 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
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34 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
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35 <options>
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36 <filter type="data_meta" ref="group" key="groups"/>
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37 </options>
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38 </param>
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39 <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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40 </inputs>
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41 <outputs>
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42 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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43 <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
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44 <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->
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45 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
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46 </collection>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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51 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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52 <output_collection name="groupfastas" count="2">
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53 <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
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54 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
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55 </output_collection>
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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
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64 **Command Documenation**
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65
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66 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups.
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67
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68 .. _group: http://www.mothur.org/wiki/Group_file
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69 .. _name: http://www.mothur.org/wiki/Name_file
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70 .. _split.groups: http://www.mothur.org/wiki/Split.groups
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71 ]]>
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72 </help>
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73 <expand macro="citations"/>
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74 </tool>