Mercurial > repos > earlhaminst > hcluster_sg

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/hcluster_sg commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb
author earlhaminst
date Mon, 10 Mar 2025 23:35:45 +0000
parents 9b7694333ba8
children
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1 <tool id="hcluster_sg" name="hcluster_sg" version="0.5.1.1">
0
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2 <description>Hierarchically clustering on a sparse graph</description>
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3 <requirements>
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4 <requirement type="package" version="0.5.1">hcluster_sg</requirement>
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5 </requirements>
3
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6 <command detect_errors="exit_code"><![CDATA[
0
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7 hcluster_sg
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8 -w $w
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9 $c_conditional.c
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10 #if $c_conditional.c == ''
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11 -s $c_conditional.s
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12 -m $c_conditional.m
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13 -b $c_conditional.b
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14 $c_conditional.O.O_selector
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15 #if $c_conditional.O.O_selector == '-O'
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16 -r $c_conditional.O.r
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17 #end if
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18 #if $c_conditional.C
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19 -C '$c_conditional.C'
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20 #end if
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21 -L $c_conditional.L
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22 #end if
2
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23 '$inputFile'
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24 > '$outputFile'
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25 ]]></command>
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26 <inputs>
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27 <param name="inputFile" type="data" format="tabular" label="Weight file" help="3-columns format: id-1 id-2 integer-weight" />
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28 <param argument="-w" type="integer" min="0" value="20" label="Minimum edge weight" />
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29 <conditional name="c_conditional">
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30 <param argument="-c" type="select" label="Only find single-linkage clusters" help="Bypass h-cluster">
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31 <option value="-c">Yes</option>
0
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32 <option value="" selected="true">No</option>
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33 </param>
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34 <when value="-c" />
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35 <when value="">
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36 <param argument="-s" type="float" value="0.5" label="Minimum edge density between a join" />
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37 <param argument="-m" type="integer" value="500" label="Maximum size" />
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38 <param argument="-b" type="float" value="0.1" label="Breaking edge density" />
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39 <conditional name="O">
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40 <param name="O_selector" argument="-O" type="select" label="Use once-fail-inactive-forever mode">
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41 <option value="-O">Yes</option>
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42 <option value="" selected="true">No</option>
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43 </param>
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44 <when value="-O">
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45 <param argument="-r" type="integer" value="5" label="Weight resolution" />
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46 </when>
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47 <when value="" />
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48 </conditional>
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49 <param argument="-C" type="data" format="tabular" optional="true" label="Category file" />
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50 <param argument="-L" type="integer" value="2" label="Stringency level" />
0
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51 </when>
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52 </conditional>
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53 </inputs>
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54 <outputs>
3
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55 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string}" />
0
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="inputFile" ftype="tabular" value="exam-1.txt" />
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60 <output name="outputFile" file="hcluster_sg1.txt" />
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61 </test>
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62 <test>
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63 <param name="inputFile" ftype="tabular" value="exam-1.txt" />
6
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64 <conditional name="c_conditional">
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65 <param name="c" value="-c" />
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66 </conditional>
0
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67 <output name="outputFile" file="hcluster_sg2.txt" />
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68 </test>
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69 </tests>
3
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70 <help><![CDATA[
5
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71 `hcluster_sg`_ is a generic tool for hierarchical or single-linkage clustering on a sparse graph.
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72 Used by the `Ensembl Compara GeneTrees`_ pipeline.
0
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73
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74 .. _hcluster_sg: https://github.com/douglasgscofield/hcluster
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75 .. _Ensembl Compara GeneTrees: https://www.ensembl.org/info/genome/compara/homology_method.html
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76 ]]></help>
0
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77 <citations>
5
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78 <citation type="doi">https://doi.org/10.1093/gigascience/giy005</citation>
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79 </citations>
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
earlhaminst
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80 </tool>