Mercurial > repos > iuc > mothur_mantel

annotate mantel.xml @ 10:d1a9a6260101 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:51:13 +0000
parents 17b471efdc40
children
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04aa7542e2df 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_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>
10
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
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12
2
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13 ## create symlinks to input datasets
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14 ln -s '$dist' dist.dat &&
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15 ln -s '$dist2' dist2.dat &&
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16
2
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17 echo 'mantel(
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18 phylip1=dist.dat,
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19 phylip2=dist2.dat,
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20 method=$method,
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21 iters=$iters
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22 )'
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23 | sed 's/ //g' ## mothur trips over whitespace
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24 | mothur
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25 | tee mothur.out.log
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26 ]]></command>
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27 <inputs>
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28 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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29 <param name="dist2" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip2 - Distance Matrix"/>
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30 <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
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31 <option value="pearson" selected="true">pearson</option>
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32 <option value="spearman">spearman</option>
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33 <option value="kendall">kendall</option>
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34 </param>
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35 <param name="iters" type="integer" value="1000" label="iters - Number of random configuration to try (default 1000)"/>
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36 <expand macro="param-savelog"/>
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37 </inputs>
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38 <outputs>
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39 <expand macro="logfile-output"/>
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40 <data name="mantel" format="tabular" from_work_dir="dist*.mantel" label="${tool.name} on ${on_string}: mantel"/>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="dist" value="veg.dist"/>
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45 <param name="dist2" value="env.dist"/>
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46 <output name="mantel" ftype="tabular">
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47 <assert_contents>
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48 <has_line_matching expression="^Mantel\tpValue$"/>
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49 </assert_contents>
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50 </output>
2
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51 <param name="savelog" value="true"/>
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52 <expand macro="logfile-test"/>
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53 </test>
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54 </tests>
2
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55 <help><![CDATA[
0
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56
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57 @MOTHUR_OVERVIEW@
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58
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59 **Command Documentation**
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60
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61 The mantel_ command calculates the Mantel correlation coefficient between two matrices_.
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62
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63 .. _matrices: //www.mothur.org/wiki/Phylip-formatted_distance_matrix
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64 .. _mantel: https://www.mothur.org/wiki/Mantel
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65
2
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66 ]]></help>
5
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67 <expand macro="citations">
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68 <expand macro="citations-ecology"/>
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69 </expand>
0
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70 </tool>