annotate hcluster_sg.xml @ 2:176639d514ee draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
author earlhaminst
date Fri, 24 Mar 2017 12:32:37 -0400
parents 4a233271d05a
children 891cc66ea91b
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4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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1 <tool id="hcluster_sg" name="hcluster_sg" version="0.5.1">
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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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>
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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5 </requirements>
2
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6 <command detect_errors="exit_code">
0
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7 <![CDATA[
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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8 hcluster_sg
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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9 -w $w
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10 -s $s
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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11 -m $m
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12 $c
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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13 -b $b
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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14 $O.O_selector
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15 #if $O.O_selector == '-O'
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16 -r $O.r
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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17 #end if
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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18 #if $C
2
176639d514ee planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
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19 -C '$C'
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4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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20 #end if
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21 -L $L
2
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22 '$inputFile'
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23 > '$outputFile'
0
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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24 ]]>
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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25 </command>
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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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" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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28 <param name="w" type="integer" min="0" value="20" label="Minimum edge weight" help="(-w)" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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29 <param name="s" type="float" value="0.5" label="Minimum edge density between a join" help="(-s)" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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30 <param name="m" type="integer" value="500" label="Maximum size" help="(-m)" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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31 <param name="c" type="boolean" truevalue="-c" falsevalue="" label="Only find single-linkage clusters" help="Bypass h-cluster (-c)" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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32 <param name="b" type="float" value="0.1" label="Breaking edge density" help="(-b)" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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33 <conditional name="O">
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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34 <param name="O_selector" type="select" label="Use once-fail-inactive-forever mode" help="(-O)">
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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35 <option value="-O">Yes</option>
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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36 <option value="" selected="true">No</option>
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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37 </param>
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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38 <when value="-O">
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39 <param name="r" type="integer" value="5" label="Weight resolution" help="(-r)" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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40 </when>
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41 <when value="" />
4a233271d05a planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg commit e24b91d3051c422ee2a20caf8bb12f0896e2c84a-dirty
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42 </conditional>
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43 <param name="C" type="data" format="tabular" optional="true" label="Category file" help="(-C)" />
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44 <param name="L" type="integer" value="2" label="Stringency level" help="(-L)" />
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45 </inputs>
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46 <outputs>
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47 <data format="tabular" name="outputFile" label="${tool.name} on ${on_string}" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="inputFile" ftype="tabular" value="exam-1.txt" />
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52 <output name="outputFile" file="hcluster_sg1.txt" />
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53 </test>
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54 <test>
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55 <param name="inputFile" ftype="tabular" value="exam-1.txt" />
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56 <param name="c" value="true" />
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57 <output name="outputFile" file="hcluster_sg2.txt" />
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62 Simple wrapper for `hcluster_sg`_.
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63
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64 .. _hcluster_sg: https://github.com/douglasgscofield/hcluster
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65 ]]>
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66 </help>
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67 <citations>
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68 </citations>
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69 </tool>