Mercurial > repos > iuc > mothur_mantel

annotate mantel.xml @ 12:19f0af1ec3d3 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 23:20:39 +0000
parents 9f7794dc9bc8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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480cdda84b44 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_mantel" name="Mantel" version="@WRAPPER_VERSION@.0">
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2 <description>Mantel correlation coefficient between two matrices.</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 '$dist' dist.dat &&
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14 ln -s '$dist2' dist2.dat &&
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16 echo 'mantel(
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17 phylip1=dist.dat,
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18 phylip2=dist2.dat,
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19 method=$method,
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20 iters=$iters
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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 | tee mothur.out.log
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25 ]]></command>
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26 <inputs>
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27 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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28 <param name="dist2" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip2 - Distance Matrix"/>
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29 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
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30 <option value="pearson" selected="true">pearson</option>
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31 <option value="spearman">spearman</option>
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32 <option value="kendall">kendall</option>
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33 </param>
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34 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
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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="mantel" format="tabular" from_work_dir="dist*.mantel" label="${tool.name} on ${on_string}: mantel"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="dist" value="veg.dist"/>
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44 <param name="dist2" value="env.dist"/>
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45 <output name="mantel" ftype="tabular">
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46 <assert_contents>
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47 <has_line_matching expression="^Mantel\tpValue$"/>
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48 </assert_contents>
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49 </output>
5
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50 <param name="savelog" value="true"/>
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51 <expand macro="logfile-test"/>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55
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56 @MOTHUR_OVERVIEW@
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57
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58 **Command Documentation**
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59
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60 The mantel_ command calculates the Mantel correlation coefficient between two matrices_.
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61
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62 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
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63 .. _mantel: https://www.mothur.org/wiki/Mantel
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64
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65 ]]></help>
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66 <expand macro="citations">
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67 <expand macro="citations-ecology"/>
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68 </expand>
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69 </tool>