annotate macros.xml @ 5:e9bd16ba5ebd draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit a272692329ad5a5c9062ec7450e73e3fdd9447e3
author iuc
date Mon, 06 Jun 2022 07:49:11 +0000
parents a315c25dc813
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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1 <macros>
5
e9bd16ba5ebd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit a272692329ad5a5c9062ec7450e73e3fdd9447e3
iuc
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2 <token name="@TOOL_VERSION@">1.2.6</token>
e9bd16ba5ebd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit a272692329ad5a5c9062ec7450e73e3fdd9447e3
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3 <token name="@VERSION_SUFFIX@">0</token>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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4 <xml name="xrefs">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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5 <xrefs>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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6 <xref type="bio.tools">purge_dups</xref>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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7 </xrefs>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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8 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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9 <xml name="trimmers">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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10 <section name="section_hist" title="Histogram plot options" >
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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11 <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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12 <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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13 <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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14 <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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15 <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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16 <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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17 </section>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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18 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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19 <token name="@HIST_PLOT@"><![CDATA[
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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20 python '$__tool_directory__/hist_plot.py'
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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21 --cutoffs cutoffs.tsv
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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22 #if $function_select.section_hist.ymin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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23 --ymin $function_select.section_hist.ymin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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24 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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25 #if $function_select.section_hist.ymax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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26 --ymax $function_select.section_hist.ymax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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27 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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28 #if $function_select.section_hist.xmin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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29 --xmin $function_select.section_hist.xmin
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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30 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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31 #if $function_select.section_hist.xmax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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32 --xmax $function_select.section_hist.xmax
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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33 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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34 #if $function_select.section_hist.title
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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35 --title '${function_select.section_hist.title}'
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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36 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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37 depth.stat hist.png
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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38 ]]></token>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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39 <token name="@CALCUTS@"><![CDATA[
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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40 calcuts
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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41 #if $function_select.section_calcuts.min_depth:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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42 -f $function_select.section_calcuts.min_depth
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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43 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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44 #if $function_select.section_calcuts.low_depth:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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45 -l $function_select.section_calcuts.low_depth
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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46 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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47 #if $function_select.section_calcuts.transition:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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48 -m $function_select.section_calcuts.transition
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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49 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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50 #if $function_select.section_calcuts.upper_depth:
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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51 -u $function_select.section_calcuts.upper_depth
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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52 #end if
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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53 $function_select.section_calcuts.ploidy
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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54 ]]></token>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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55 <xml name="calcuts">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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56 <section name="section_calcuts" title="Calcuts options" expanded="true">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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57 <param argument="-f" name="min_depth" type="float" min="0" max="1" value="0.1" label="Minimum depth count fraction to maximum depth count"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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58 <param argument="-l" name="low_depth" type="integer" min="0" optional="true" label="Lower bound for read depth" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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59 <param argument="-m" name="transition" type="integer" min="0" optional="true" label="Transition between haploid and diploid"/>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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60 <param argument="-u" name="upper_depth" type="integer" min="0" optional="true" label="Upper bound for read depth" />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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61 <param name="ploidy" argument="-d" type="select" label="Ploidy" help="Treat as haploid assembly or diploid assembly">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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62 <option value="-d 0" selected="true">Diploid</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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63 <option value="-d 1">Haploid</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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64 </param>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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65 </section>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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66 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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67 <xml name="output_macro">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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68 <param name="output_options" type="select" multiple="true" display="checkboxes" label="Output files">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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69 <yield />
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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70 <option value="histogram" selected="true">Histogram plot</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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71 <option value="calcuts_cutoff" selected="true">Calcuts cutoff</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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72 <option value="calcuts_log">Calcuts log</option>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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73 </param>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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74 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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75 <xml name="requirements">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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76 <requirements>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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77 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
5
e9bd16ba5ebd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit a272692329ad5a5c9062ec7450e73e3fdd9447e3
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78 <requirement type="package" version="3.5.2">matplotlib-base</requirement>
4
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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79 </requirements>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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80 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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81 <xml name="citations">
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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82 <citations>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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83 <citation type="doi">10.1093/bioinformatics/btaa025</citation>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
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84 </citations>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
iuc
parents:
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85 </xml>
a315c25dc813 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit d2ef7bd6598695a681446eaf9c5b8c142e8a0199"
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86 </macros>