Mercurial > repos > iuc > scoary

annotate scoary.xml @ 0:42a1a5750539 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
author iuc
date Sun, 21 Mar 2021 12:21:41 +0000
parents
children 77d50ec2bcf2
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42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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1 <tool id="scoary" name="Scoary" version="@TOOL_VERSION@+galaxy0" profile="20.01">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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2 <description>calculates the assocations between all genes in the accessory genome and the traits</description>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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3 <macros>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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4 <token name="@TOOL_VERSION@">1.6.16</token>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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5 </macros>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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6 <requirements>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">scoary</requirement>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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8 </requirements>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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9 <version_command>scoary --version</version_command>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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10 <command detect_errors="exit_code"><![CDATA[
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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11 scoary
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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12
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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13 ###########
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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14 ## Input ##
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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15 ###########
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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16
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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17 -t '$input_traits'
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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18 -g '$input_genes'
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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19
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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20 #if $input_restricts:
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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21 -r '$input_restricts'
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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22 #end if
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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24 ########################
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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25 ## Additional Options ##
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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26 ########################
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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27
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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28 #if len($additional_options.series_pc) != 0
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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29 -p #echo " ".join([ "'%s'" % $s.pvalue for $i, $s in enumerate($additional_options.series_pc) ])
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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30 -c #echo " ".join([ "'%s'" % $s.correction for $i, $s in enumerate($additional_options.series_pc) ])
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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31 #end if
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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32
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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33 #if $additional_options.permute != 0:
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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34 -e str($additional_options.permute)
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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35 #end if
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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36
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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37 #if $additional_options.maxhits != 0:
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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38 -m str($additional_options.maxhits)
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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39 #end if
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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40
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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41 $additional_options.collapse
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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42 $output_options.upgma
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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43
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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44 #if $input_newicktree:
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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45 -n '$input_newicktree'
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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46 #end if
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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47
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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48 #########
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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49 ## END ##
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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50 #########
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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51
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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52 --no-time
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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53 &&
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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54 tail -n +1 *.csv | sed "s/\,/\\t/g" > scoary_output.tsv &&
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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55 mv *.nwk scoary_output.nwk
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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56
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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57 ]]></command>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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58 <inputs>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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59 <param name="input_traits" argument="-t" type="data" format="csv" label="Trait table"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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60 <param name="input_genes" argument="-g" type="data" format="csv" label="Gene Presence/Absence table from ROARY (default output)"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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61 <param name="input_restricts" optional="true" argument="-r" type="data" format="tabular" label="Table to analyze a subset of strains" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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62
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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63 <!-- Additional Options -->
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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64 <section name="additional_options" title="Additional Options">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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65 <repeat name="series_pc" title="P-value cutoff(s) and Correction(s)">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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66 <param name="pvalue" argument="-p" type="float" min="0" max="1.0" value="0.05" label="P-value cutoff for one Trait" help="SCOARY will not report genes with higher p-values than this (Default=1.0=All). Provide a single value (applied to all) or exactly as many values as correction criteria and in corresponding order (e.g., 0.05 0.05 for two traits)."/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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67 <param name="correction" argument="-c" type="select" label="P-value correction" help="Apply the p-value corrections to the p-value cutoffs you have entered (Default = Individual p-value)." >
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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68 <option value="I" selected="true">Individual (naive) p-value</option>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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69 <option value="B">Bonferroni adjusted p-value</option>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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70 <option value="BH">Benjamini-Hochberg adjusted p</option>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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71 <option value="PW">Best (lowest) pairwise comparison</option>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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72 <option value="EPW">Entire range of pairwise comparison p-values</option>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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73 <option value="P">Empirical p-value from permutations</option>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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74 </param>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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75 </repeat>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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76 <param name="permute" argument="-e" type="integer" min="0" value="0" label="Permutations" help="Perform N number of permutations of the significant results post-analysis. (Default = 0 = None)" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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77 <param name="maxhits" argument="-m" type="integer" min="0" value="0" label="Maximal number of hits to report" help="SCOARY will only report the top max hits results per trait. (Default = 0 = All)" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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78 <param name="collapse" argument="--collapse" type="boolean" checked="false" truevalue="--collapse" falsevalue="" label="Collapse correlated genes" help="Collapse correlated genes (genes that have identical distribution patterns in the sample) into merged units. (Default=false)"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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79 <param name="input_newicktree" optional="true" argument="-n" type="data" format="newick" label="Supply a custom tree (Newick format) for phylogenetic analyses instead instead of calculating it internally." />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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80 </section>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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81
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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82 <!-- Output Options -->
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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83 <section name="output_options" title="Output Options" expanded="true">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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84 <param name="upgma" argument="-u" type="boolean" checked="false" truevalue="-u" falsevalue="" label="UPGMA tree" help="Calculate UPGMA tree to a newick file."/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
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85 </section>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
86 </inputs>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
87 <outputs>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
88 <data name="out_tabular" format="tabular" from_work_dir="scoary_output.tsv" label="${tool.name} on ${on_string}: Table" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
89 <data name="out_newick" format="newick" from_work_dir="scoary_output.nwk" label="${tool.name} on ${on_string}: Tree">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
90 <filter>(output_options['upgma'] is True)</filter>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
91 </data>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
92 </outputs>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
93 <tests>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
94 <test expect_num_outputs="2">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
95 <param name="input_traits" ftype="csv" value="Tetracycline_resistance.csv" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
96 <param name="input_genes" ftype="csv" value="Gene_presence_absence.csv" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
97 <param name="upgma" value="Yes" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
98 <repeat name="series_pc">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
99 <param name="pvalue" value="0.05"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
100 <param name="correction" value="I"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
101 </repeat>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
102 <output name="out_tabular" file="scoary_output.tsv" ftype="tabular" sort="true">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
103 <assert_contents>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
104 <has_n_lines n="573" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
105 <has_line line="==&gt; Bogus_trait.results.csv &lt;==" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
106 <has_line line="==&gt; Tetracycline_resistance.results.csv &lt;==" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
107 </assert_contents>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
108 </output>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
109 <output name="out_newick" file="scoary_output.nwk" ftype="newick" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
110 </test>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
111 <test expect_num_outputs="2">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
112 <param name="input_traits" ftype="csv" value="Tetracycline_resistance.csv" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
113 <param name="input_genes" ftype="csv" value="Gene_presence_absence.csv" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
114 <param name="upgma" value="Yes" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
115 <repeat name="series_pc">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
116 <param name="pvalue" value="0.05"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
117 <param name="correction" value="I"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
118 </repeat>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
119 <repeat name="series_pc">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
120 <param name="pvalue" value="0.05"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
121 <param name="correction" value="EPW"/>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
122 </repeat>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
123 <output name="out_tabular" file="scoary_output_2.tsv" ftype="tabular" sort="true">
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
124 <assert_contents>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
125 <has_n_lines n="27" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
126 <has_line line="==&gt; Bogus_trait.results.csv &lt;==" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
127 <has_line line="==&gt; Tetracycline_resistance.results.csv &lt;==" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
128 </assert_contents>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
129 </output>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
130 <output name="out_newick" file="scoary_output_2.nwk" ftype="newick" />
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
131 </test>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
132 </tests>
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
133
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
134 <help><![CDATA[
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
135
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
136 .. class:: infomark
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
137
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
138 **What it does**
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
139
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
140 -------------------
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
141
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
142 **Scoary**
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
143
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
144 Scoary is designed to take the csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
145
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
146 -------------------
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
147
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
148 **Inputs**
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
149
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
150 -------------------
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
151
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
152 Scoary requires two input files: csv file from Roary and a list of traits to test associations to.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
153 Traits can be anything as long as you can classify it into binary categories (e.g. antibiotic resistance, group membership (yes/no), MIC value higher/lower than 16).
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
154 Make sure you your entires are separated by ','.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
155 The traits file needs to be formatted in a specific way (please take a look into the (documentation)[https://github.com/AdmiralenOla/Scoary]).
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
156
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
157 You can also use as input the pan-genome as called from Jason Sahl's program LS-BSR (Large-Scale Blast Score Ratio).
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
158 The program includes a python script for converting LS-BSR output to the Roary/Scoary format.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
159
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
160 Trait presence is indicated by 1, trait absence by 0.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
161 Assumes strain names in the first column and trait names in the first row.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
162
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
163 Input gene presence/absence table (comma-separated-values) from ROARY.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
164 Strain names must be equal to those in the trait table.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
165
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
166 -----------
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
167
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
168 **Outputs**
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
169
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
170 -----------
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
171
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
172 Scory outputs a single csv traits file. It uses comma "," as a delimiter.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
diff changeset
173 The results consists of genes that were found to be associated with the trait, sorted according to significance.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
parents:
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174 By default, Scoary reports all genes with a naive p-value < 0.05.
42a1a5750539 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary commit ce823d6021a7afbc2c49ba60e32faababaffd870"
iuc
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175
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176 You can find the description of the columns in the (documentation)[https://github.com/AdmiralenOla/Scoary].
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177
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178 --------------------
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179
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180 **More Information**
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181
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182 --------------------
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183
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184 See the excellent `Scoary documentation`_
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185
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186 .. _`Scoary documentation`: https://github.com/AdmiralenOla/Scoary
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187
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188
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189 **P-value cutoff (-p)**: For Fishers, Bonferronis, and Benjamini-Hochbergs tests, SCOARY will not report genes with higher p-values than this.
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190 For empirical p-values, this is treated as an alpha level instead.
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191 I.e. 0.02 will filter all genes except the lower and upper percentile from this test.
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192 Run with "-p 1.0" to report all genes. Accepts standard form (e.g. 1E-8).
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193 Provide a single value (applied to all) or exactly as many values as correction criteria and in corresponding order (e.g., 0.05 0.1 0.05 0.02).
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194
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195 **Correction (-c)**: Apply the indicated filtration measure: I=Individual (naive) p-value, B=Bonferroni adjusted p-value, BH=Benjamini-Hochberg adjusted p, PW=Best (lowest) pairwise comparison, EPW=Entire range of pairwise comparison p-values, P=Empirical p-value from permutations.
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196 You can enter as many correction criteria as you would like.
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197 These will be associated with the p-value cutoffs you enter.
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198 For example "-c I EPW -p 0.1 0.05" will apply the following cutoffs: Naive p-value must be lower than 0.1 AND the entire range of pairwise comparison values are below 0.05 for this gene.
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199 Note that the empirical p-values should be interpreted at both tails.
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200 Therefore, running "-c P -p 0.05" will apply an alpha of 0.05 to the empirical (permuted) p-values, i.e. it will filter everything except the upper and lower 2.5 percent of the distribution.
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201
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202 **Permute (-e)**: Perform N number of permutations of the significant results post-analysis.
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203 Each permutation will do a label switching of the phenotype and a new p-value is calculated according to this new dataset.
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204 After all N permutations are completed, the results are ordered in ascending order, and the percentile of the original result in the permuted p-value distribution is reported.
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205
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206 --------------------
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207
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208 **Galaxy Wrapper Development**
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209
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210 --------------------
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211
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212 Author: Florian Heyl
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213
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214 ]]></help>
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215 <citations>
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216 <citation type="doi">10.1038/s41467-020-15171-6</citation>
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217 </citations>
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218 </tool>