Mercurial > repos > brinkmanlab > mcl
annotate mcl.xml @ 0:60609b076830 draft default tip
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
author | brinkmanlab |
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date | Fri, 24 Jan 2020 18:05:36 -0500 |
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0
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
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1 <tool id="mcl" name="MCL" version="14.137" profile="16.04"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
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2 <description>The Markov Cluster Algorithm, a cluster algorithm for graphs</description> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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3 <edam_topics> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
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4 <edam_topic>topic_3570</edam_topic> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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5 </edam_topics> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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6 <edam_operations> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
brinkmanlab
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7 <edam_operation>operation_3432</edam_operation> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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8 </edam_operations> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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9 <requirements> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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10 <requirement type="package" version="14.137">mcl</requirement> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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11 </requirements> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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12 <version_command>mcl --version</version_command> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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13 <command detect_errors="aggressive"><![CDATA[ |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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14 mcl $input_type_select.input -I $inflation $input_type_select.input_type -V all -te \${GALAXY_SLOTS:-1} $sum_loops $discard_loops |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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15 #if $verbosity |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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16 #for $v in $verbosity |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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17 -v $v |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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18 #end for |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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19 #end if |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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20 #if $reweight and $reweight != 1.0 |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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21 -c $reweight |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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22 #end if |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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23 #if $transform |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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24 #if $input_type_select.input_type == "--abc" |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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25 -abc-tf "$transform" |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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26 #else if $input_type_select.input_type == "" |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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27 -tf "$transform" |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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28 #end if |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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29 #end if |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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30 -o $output |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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31 ]]></command> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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32 <inputs> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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33 <conditional name="input_type_select"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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34 <param name="input_type" type="select" argument="--abc" label="Input Type"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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35 <option value="--abc" selected="true">Labeled</option> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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36 <option value="--sif">SIF</option> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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37 <option value="">Matrix</option> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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38 </param> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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39 <when value=""> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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40 <param type="data" format="mclmat" name="input" argument="input" label="Input" optional="false"/> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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41 </when> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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42 <when value="--abc"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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43 <param type="data" format="tabular" name="input" argument="input" label="Input" optional="false"/> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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44 </when> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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45 <when value="--sif"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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46 <param type="data" format="sif" name="input" argument="input" label="Input" optional="false"/> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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47 </when> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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48 </conditional> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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49 <param name="inflation" type="float" value="4.0" label="Inflation" help="This value is the main handle for affecting cluster granularity. It is usually chosen somewhere in the range [1.2-5.0]. -I 5.0 will tend to result in fine-grained clusterings, and -I 1.2 will tend to result in very coarse grained clusterings. Your mileage will vary depending on the characteristics of your data. That is why it is a good idea to test the quality and coherency of your clusterings using clm dist and clm info. This will most likely reveal that certain values of -I are simply not right for your data." /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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50 <param name="transform" type="text" area="true" label="Transform input matrix values" help="See https://micans.org/mcl/man/mcxio.html#trans for the transformation syntax" /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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51 <param name="discard_loops" type="boolean" checked="true" truevalue="" falsevalue="--discard-loops=n" argument="--discard-loops" label="Discard loops in input" help="Remove any loops that are present in the input. Bear in mind that loops will still be modified in all cases where the loop weight is not maximal among the list of edge weights for a given node." /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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52 <param name="sum_loops" type="boolean" checked="false" truevalue="--sum-loops" falsevalue="" argument="--sum-loops" label="Set loops to sum of other arcs weights" /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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53 <param name="reweight" type="float" value="1" argument="-c" optional="true" label="Reweight loops" help="As the final step of loop computation (i.e. after initialization and shadowing) all loop weights are multiplied by the provided value." /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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54 <param name="verbosity" type="select" multiple="true" optional="true" label="Verbosity"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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55 <option value="pruning">pruning</option> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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56 <option value="explain">explain</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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57 <option value="cls">cls</option> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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58 </param> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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59 </inputs> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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60 <outputs> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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61 <data format="txt" name="output"> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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62 <change_format> |
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63 <when input="input_type_select.input_type" value="" format="mclmat" /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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64 <when input="input_type_select.input_type" value="--abc" format="tabular" /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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65 <when input="input_type_select.input_type" value="--sif" format="tabular" /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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66 </change_format> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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67 </data> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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68 </outputs> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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69 <tests> |
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"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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70 <test expect_num_outputs="1"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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71 <conditional name="input_type_select"> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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72 <param name="input_type" value="--abc" /> |
60609b076830
"planemo upload for repository https://github.com/brinkmanlab/galaxy-tools/tree/master/mcl commit 33b02e08cbc8f76fb4b8537f8c968393f85a1b5e-dirty"
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73 <param name="input" value="test-data/mash-dist.tabular" ftype="tabular" /> |
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74 </conditional> |
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75 <param name="transform" value="mul(-1),add(1),gq(0.96)" /> |
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76 <output name="output" file="test-data/mash-dist-cluster.tabular" ftype="tabular" /> |
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77 </test> |
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78 </tests> |
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79 <help> |
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80 https://micans.org/mcl/man/mcl.html |
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81 </help> |
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82 <citations> |
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83 <citation type="doi">10.5281/zenodo.3364789</citation> |
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84 <citation type="bibtex"><![CDATA[ |
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85 @article{dongen29graph, |
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86 title={Graph Clustering by Flow Simulation. 2000}, |
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87 author={Dongen, SV}, |
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88 journal={Domplein}, |
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89 volume={29}, |
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90 pages={3512} |
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91 } |
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92 ]]></citation> |
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93 <citation type="doi">10.1093/nar/30.7.1575</citation> |
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94 </citations> |
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95 </tool> |