Mercurial > repos > iuc > purge_dups

annotate purge_dups.xml @ 3:76d4cbefff85 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
author iuc
date Mon, 14 Jun 2021 18:01:05 +0000
parents 17b378303f2d
children a315c25dc813
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rev   line source
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
1 <tool id="purge_dups" name="Purge overlaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
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2 <description>and haplotigs in an assembly based on read depth (purge_dups)</description>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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3 <macros>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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4 <token name="@TOOL_VERSION@">1.2.5</token>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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5 <token name="@VERSION_SUFFIX@">3</token>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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6 <xml name="trimmers">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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7 <section name="section_hist" title="Histogram plot options" >
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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8 <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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9 <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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10 <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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11 <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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12 <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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13 <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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14 </section>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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15 </xml>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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16 <token name="@HIST_PLOT@"><![CDATA[
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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17 python '$__tool_directory__/hist_plot.py'
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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18 --cutoffs cutoffs.tsv
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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19 #if $function_select.section_hist.ymin
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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20 --ymin $function_select.section_hist.ymin
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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21 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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22 #if $function_select.section_hist.ymax
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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23 --ymax $function_select.section_hist.ymax
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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24 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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25 #if $function_select.section_hist.xmin
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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26 --xmin $function_select.section_hist.xmin
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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27 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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28 #if $function_select.section_hist.xmax
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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29 --xmax $function_select.section_hist.xmax
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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30 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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31 #if $function_select.section_hist.title
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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32 --title '${function_select.section_hist.title}'
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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33 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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34 depth.stat hist.png
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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35 ]]></token>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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36 <token name="@CALCUTS@"><![CDATA[
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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37 calcuts
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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38 #if $function_select.section_calcuts.min_depth:
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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39 -f $function_select.section_calcuts.min_depth
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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40 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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41 #if $function_select.section_calcuts.low_depth:
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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42 -l $function_select.section_calcuts.low_depth
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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43 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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44 #if $function_select.section_calcuts.transition:
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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45 -m $function_select.section_calcuts.transition
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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46 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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47 #if $function_select.section_calcuts.upper_depth:
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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48 -u $function_select.section_calcuts.upper_depth
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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49 #end if
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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50 $function_select.section_calcuts.ploidy
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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51 ]]></token>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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52 <xml name="calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
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53 <section name="section_calcuts" title="Calcuts options">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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54 <param name="min_depth" type="float" label="Minimum depth count fraction to maximum depth coun" min="0" max="1" argument="-f" optional="true" help="Default = 0.1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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55 <param name="low_depth" label="Lower bound for read depth" type="integer" argument="-l" optional="true"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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56 <param name="transition" label="Transition between haploid and diploid" type="integer" argument="-m" optional="true"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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57 <param name="upper_depth" label="Upper bound for read depth" type="integer" argument="-u" optional="true"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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58 <param name="ploidy" argument="-d" type="select" label="Ploidy">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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59 <option value="-d 0" selected="true">Diploid [0]</option>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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60 <option value="-d 1">Haploid [1]</option>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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61 </param>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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62 </section>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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63 </xml>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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64 </macros>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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65 <requirements>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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66 <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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67 <requirement type="package" version="3.4.2">matplotlib-base</requirement>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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68 </requirements>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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69 <command detect_errors="exit_code"><![CDATA[
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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70 #if $function_select.functions == 'purge_dups':
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
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71 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
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72 #if $file.is_of_type("paf"):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
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73 gzip -c '${file}' > '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
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74 #else
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
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75 ln -s '${file}' '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
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76 #end if
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
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77 #end for
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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78 purge_dups
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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79 #if $function_select.coverage:
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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80 -c '${function_select.coverage}'
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
81 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
82 #if $function_select.cutoffs:
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
83 -T '${function_select.cutoffs}'
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
84 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
85 #if $function_select.min_bad:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
86 -f $function_select.min_bad
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
87 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
88 #if $function_select.min_align:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
89 -a $function_select.min_align
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
90 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
91 #if $function_select.min_match:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
92 -b $function_select.min_match
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
93 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
94 #if $function_select.min_chain:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
95 -m $function_select.min_chain
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
96 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
97 #if $function_select.max_gap:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
98 -M $function_select.max_gap
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
99 #end if
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
100 #if $function_select.double_chain.chaining_rounds == 'two':
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
101 -2
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
102 #if $function_select.double_chain.max_gap_2:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
103 -G $function_select.double_chain.max_gap_2
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
104 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
105 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
106 #if $function_select.min_chain_score:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
107 -l $function_select.min_chain_score
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
108 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
109 #if $function_select.max_extend:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
110 -E $function_select.max_extend
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
111 #end if
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
112 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
113 '${i}.gz'
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
114 #end for
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
115 > dups.bed 2> purge_dups.log
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
116 #else if $function_select.functions == 'split_fa':
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
117 split_fa
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
118 #if $function_select.split:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
119 -n $function_select.split
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
120 #end if
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
121 '${function_select.input}' > split.fasta
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
122 #else if $function_select.functions == 'pbcstat':
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
123 #for $i, $file in enumerate($function_select.input):
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
124 #if $file.is_of_type('paf'):
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
125 gzip -c '${file}' > '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
126 #else
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
127 ln -s '${file}' '${i}.gz' &&
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
128 #end if
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
129 #end for
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
130 pbcstat
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
131 #if $function_select.max_cov:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
132 -M $function_select.max_cov
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
133 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
134 #if $function_select.min_map_ratio:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
135 -f $function_select.min_map_ratio
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
136 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
137 #if $function_select.min_map_qual:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
138 -q $function_select.min_map_qual
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
139 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
140 #if $function_select.flank:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
141 -l $function_select.flank
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
142 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
143 $function_select.primary_alignments
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
144
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
145 #for $i, $file in enumerate($function_select.input):
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
146 '${i}.gz'
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
147 #end for
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
148 && mv PB.stat depth.stat
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
149 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
150 && @HIST_PLOT@
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
151
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
152 #else if $function_select.functions == 'ngscstat':
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
153 ngscstat
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
154 #if $function_select.min_align_qual:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
155 -q $function_select.min_align_qual
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
156 #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
157 ## #if $function_select.max_depth:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
158 ## -M $function_select.max_depth
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
159 ## #end if
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
160 #if $function_select.max_insert:
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
161 -L $function_select.max_insert
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
162 #end if
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
163 '${function_select.input}'
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
164 && mv TX.stat depth.stat
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
165 && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
166 && @HIST_PLOT@
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
167
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
168 #else if $function_select.functions == 'calcuts':
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169 @CALCUTS@ '${function_select.input}' > cutoffs.tsv 2>calcuts.log
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170
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171 #else if $function_select.functions == 'get_seqs':
0
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172 get_seqs
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173 $function_select.coverage
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174 $function_select.haplotigs
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175 $function_select.end_trim
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176 $function_select.split
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177 #if $function_select.length:
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178 -l $function_select.length
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179 #end if
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180 #if $function_select.min_ratio:
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181 -m $function_select.min_ratio
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182 #end if
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183 #if $function_select.min_gap:
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184 -g $function_select.min_gap
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185 #end if
3
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186 '${function_select.bed_input}' '${function_select.fasta_input}'
0
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187 #end if
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188 ]]></command>
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189 <inputs>
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190 <conditional name="function_select">
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191 <param type="select" name="functions" label="Select the purge_dups function">
3
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192 <option value="purge_dups">Purge haplotigs and overlaps for an assembly (purge_dups)</option>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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193 <option value="split_fa">Split FASTA file by 'N's (split_fa)</option>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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194 <option value="pbcstat">Calculate coverage cutoff and create read depth histogram and base-levelread depth for PacBio data (calcuts+pbcstats)</option>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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195 <option value="ngscstat">Calculate coverage cutoff and create read depth histogram and base-level read detph for Illumina data (calcuts+ngscstat)</option>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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196 <option value="calcuts">calculate coverage cutoffs (calcuts)</option>
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197 <option value="get_seqs">Obtain seqeuences after purging (get_seqs)</option>
0
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198 </param>
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199 <when value="purge_dups">
2
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200 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
0
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201 <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" />
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202 <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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203 <param name="min_bad" type="float" min="0" max="1" argument="-f" optional="true" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence" help="Default = 0.8"/>
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204 <param name="min_align" type="integer" label="Minimum alignment score" argument="-a" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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205 <param name="min_match" type="integer" label="Minimum max match score" argument="-b" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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206 <param name="min_chain" label="Minimum matching bases for chaining" type="integer" argument="-m" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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207 <param name="max_gap" label="Maximum gap size for chaining" type="integer" argument="-M" optional="true"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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208 <conditional name="double_chain">
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209 <param type="select" name="chaining_rounds" label="Rounds of chaining">
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210 <option value="one">1 round</option>
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211 <option value="two">2 rounds</option>
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212 </param>
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213 <when value="two">
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214 <param name="max_gap_2" argument="-G" optional="true" label="Maximum gap size for second round of chaining" type="integer"/>
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215 </when>
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216 <when value="one"/>
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217 </conditional>
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218 <param name="min_chain_score" argument="-l" optional="true" label="Minimum chaining score for a match" type="integer" />
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219 <param name="max_extend" argument="-E" optional="true" label="Maximum extension for contig ends" type="integer" />
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220 </when>
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221 <when value="split_fa">
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222 <param name="input" type="data" format="fasta" label="Base-level coverage file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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223 <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" />
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224 </when>
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225 <when value="pbcstat">
2
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226 <param name="input" type="data" format="paf,paf.gz" multiple="true" label="PAF input file"/>
0
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227 <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/>
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228 <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/>
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229 <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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230 <param name="flank" type="integer" argument="-l" optional="true" label="Flanking space" />
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231 <param name="primary_alignments" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="true" label="Use only primary alignments" />
3
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232 <expand macro="calcuts" />
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233 <expand macro="trimmers"/>
0
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234 </when>
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235 <when value="ngscstat">
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236 <param name="input" type="data" format="bam" label="BAM input file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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237 <param name="min_align_qual" type="integer" argument="-q" optional="true" label="Minimum alignment quality" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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238 <!-- Param exists in help text, but isn't actually part of the code. Maybe in the next release? -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
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239 <!-- <param name="max_depth" type="integer" label="Maximum read depth" argument="-M" optional="true"/> -->
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240 <param name="max_insert" type="integer" argument="-L" optional="true" label="Maximum insert size"/>
3
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241 <expand macro="calcuts" />
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242 <expand macro="trimmers"/>
0
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243 </when>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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244
0
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245 <when value="calcuts">
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246 <param name="input" type="data" format="tabular" label="STAT input file"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
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247 <expand macro="calcuts" />
0
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248 </when>
3
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249
0
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diff changeset
250 <when value="get_seqs">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
251 <param name="fasta_input" type="data" format="fasta" label="Fasta input file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
252 <param name="bed_input" type="data" format="bed" label="Bed input file"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
253 <param name="coverage" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Keep high coverage contigs in the primary contig set"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
254 <param name="haplotigs" type="boolean" argument="-a" truevalue="-a" falsevalue="" checked="false" label="Do not add prefix to haplotigs"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
255 <param name="length" type="integer" argument="-l" optional="true" label="Minimum primary contig length" help="Default: 1000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
256 <param name="min_ratio" type="float" min="0" max="1" argument="-m" optional="true" label="Minimum ratio of remaining primary contig length to the original contig length"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
257 <param name="end_trim" type="boolean" argument="-e" truevalue="-e" falsevalue="" checked="true" label="Trim end sequences" help="Only remove sequences at end of halplotigs If you also want to remove the duplications in the middle, set to false, however that may delete false positive duplications."/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
258 <param name="split" type="boolean" argument="-s" truevalue="-s" falsevalue="" checked="false" label="Split contigs"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
259 <param name="min_gap" type="integer" argument="-g" optional="true" help="default=10k" label="Minimum gap size between duplications" />
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
260 </when>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
261 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
262 </inputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
263 <outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
264 <!-- Get Seqs -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
265 <data name="get_seqs_hap" format="fasta" from_work_dir="hap.fa" label="${tool.name} on ${on_string}: get seqs haplotype fasta" >
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
266 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
267 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
268 <data name="get_seqs_purged" format="fasta" from_work_dir="purged.fa" label="${tool.name} on ${on_string}: get seqs purged fasta">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
269 <filter>function_select['functions'] == 'get_seqs'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
270 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
271 <!-- Split FA -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
272 <data name="split_fasta" format="fasta" from_work_dir="split.fasta" label="${tool.name} on ${on_string}: split fasta">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
273 <filter>function_select['functions'] == 'split_fa'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
274 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
275 <!-- Ngscstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
276 <data name="ngscstat_cov" format="tabular" from_work_dir="TX.base.cov" label="${tool.name} on ${on_string}: ngscstat base coverage file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
277 <filter>function_select['functions'] == 'ngscstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
278 </data>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
279 <data name="stat_file" format="tabular" from_work_dir="depth.stat" label="${tool.name} on ${on_string}: stat file">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
280 <filter>function_select['functions'] == 'ngscstat' or function_select['functions'] == 'pbcstat'</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
281 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
282 <!-- Pbcstat -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
283 <data name="pbcstat_cov" format="tabular" from_work_dir="PB.base.cov" label="${tool.name} on ${on_string}: pbcstat base coverage file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
284 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
285 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
286 <data name="pbcstat_wig" format="wig" from_work_dir="PB.cov.wig" label="${tool.name} on ${on_string}: pbcstat base wig file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
287 <filter>function_select['functions'] == 'pbcstat'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
288 </data>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
289
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
290 <data name="hist" format="png" from_work_dir="hist.png" label="${tool.name} on ${on_string}: histogram plot">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
291 <filter>function_select['functions'] == 'pbcstat' or function_select['functions'] == 'ngscstat'</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
292 </data>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
293
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
294 <!-- Calcuts -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
295 <data name="calcuts_log" format="txt" from_work_dir="calcuts.log" label="${tool.name} on ${on_string}: calcuts log file">
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
296 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
297 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
298 <data name="calcuts_tab" format="tabular" from_work_dir="cutoffs.tsv" label="${tool.name} on ${on_string}: calcuts cutoff file">
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
299 <filter>function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts')</filter>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
300 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
301 <!-- Purge dups -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
302 <data name="purge_dups_log" format="txt" from_work_dir="purge_dups.log" label="${tool.name} on ${on_string}: purge_dups log file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
303 <filter>function_select['functions'] == 'purge_dups'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
304 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
305 <data name="purge_dups_bed" format="bed" from_work_dir="dups.bed" label="${tool.name} on ${on_string}: purge_dups bed file">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
306 <filter>function_select['functions'] == 'purge_dups'</filter>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
307 </data>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
308 </outputs>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
309 <tests>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
310 <!-- Purge dups -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
311 <test expect_num_outputs="2">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
312 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
313 <param name="functions" value="purge_dups"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
314 <param name="input" value="test.paf"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
315 <param name="coverage" value="test.cov" ftype="tabular"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
316 <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
317 <param name="min_bad" value="0.01"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
318 <param name="min_align" value="10"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
319 <param name="min_match" value="100"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
320 <param name="min_chain" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
321 <param name="max_gap" value="1000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
322 <conditional name="double_chain">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
323 <param name="chaining_rounds" value="two"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
324 <param name="max_gap_2" value="1001"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
325 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
326 <param name="min_chain_score" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
327 <param name="max_extend" value="100"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
328 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
329 <output name="purge_dups_bed" value="purge_dups_out.bed"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
330 </test>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
331 <!-- Purge dups gzip -->
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
332 <test expect_num_outputs="2">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
333 <conditional name="function_select">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
334 <param name="functions" value="purge_dups"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
335 <param name="input" value="test.paf.gz" ftype="paf.gz"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
336 <param name="coverage" value="test.cov" ftype="tabular"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
337 <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
338 <param name="min_bad" value="0.01"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
339 <param name="min_align" value="10"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
340 <param name="min_match" value="100"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
341 <param name="min_chain" value="1"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
342 <param name="max_gap" value="1000"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
343 <conditional name="double_chain">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
344 <param name="chaining_rounds" value="two"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
345 <param name="max_gap_2" value="1001"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
346 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
347 <param name="min_chain_score" value="1"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
348 <param name="max_extend" value="100"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
349 </conditional>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
350 <output name="purge_dups_bed" value="purge_dups_out.bed"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
351 </test>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
352 <!-- Purge dups multiple input -->
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
353 <test expect_num_outputs="2">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
354 <conditional name="function_select">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
355 <param name="functions" value="purge_dups"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
356 <param name="input" value="test.paf,test2.paf.gz"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
357 </conditional>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
358 <output name="purge_dups_bed" value="purge_dups_out_2.bed"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
359 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
360 <!-- Split fa -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
361 <test expect_num_outputs="1">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
362 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
363 <param name="functions" value="split_fa"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
364 <param name="input" value="test.fasta"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
365 <param name="split" value="-n"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
366 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
367 <output name="split_fasta" value="split_out.fasta"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
368 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
369 <!-- pbcstat -->
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
370 <test expect_num_outputs="6">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
371 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
372 <param name="functions" value="pbcstat"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
373 <param name="input" value="test.paf"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
374 <param name="max_cov" value="1000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
375 <param name="min_map_ratio" value="0.01"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
376 <param name="min_map_qual" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
377 <param name="flank" value="1"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
378 <param name="primary_alignments" value="-p"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
379 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
380 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
381 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
382 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
383 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
384 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
385 </section>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
386 </conditional>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
387 <output name="calcuts_tab" value="calcuts_out.tsv"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
388 <output name="pbcstat_cov" value="out.cov"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
389 <output name="pbcstat_wig" value="out.wig"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
390 <output name="stat_file" value="pbcstats.tabular"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
391 <output name="hist" value="hist.png" ftype="png" compare="sim_size"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
392 </test>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
393 <!-- pbcstat gzip -->
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
394 <test expect_num_outputs="6">
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
395 <conditional name="function_select">
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
396 <param name="functions" value="pbcstat"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
397 <param name="input" value="test.paf.gz" ftype="paf.gz"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
398 <param name="max_cov" value="1000"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
399 <param name="min_map_ratio" value="0.01"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
400 <param name="min_map_qual" value="1"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
401 <param name="flank" value="1"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
402 <param name="primary_alignments" value="-p"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
403 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
404 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
405 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
406 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
407 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
408 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
409 </section>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
410 </conditional>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
411 <output name="calcuts_tab" value="calcuts_out.tsv"/>
1
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
412 <output name="pbcstat_cov" value="out.cov"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
413 <output name="pbcstat_wig" value="out.wig"/>
29151e779524 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
iuc
parents: 0
diff changeset
414 </test>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
415 <!-- Pbcstat multiple input -->
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
416 <test expect_num_outputs="6">
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
417 <conditional name="function_select">
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
418 <param name="functions" value="pbcstat"/>
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
419 <param name="input" value="test.paf,test2.paf.gz"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
420 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
421 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
422 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
423 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
424 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
425 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
426 </section>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
427 </conditional>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
428 <output name="calcuts_tab" value="calcuts_out.tsv"/>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
429 <output name="pbcstat_cov" value="out2.cov"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
430 <output name="stat_file" value="pbcstats2.tabular"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
431 <output name="pbcstat_wig" value="out2.wig"/>
2
17b378303f2d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149"
iuc
parents: 1
diff changeset
432 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
433 <!-- ngscstat -->
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
434 <test expect_num_outputs="5">
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
435 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
436 <param name="functions" value="ngscstat"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
437 <param name="input" value="test.bam"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
438 <param name="min_align_qual" value="10"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
439 <param name="max_insert" value="100"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
440 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
441 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
442 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
443 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
444 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
445 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
446 </section>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
447 </conditional>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
448 <output name="calcuts_tab" value="calcuts_out.tsv"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
449 <output name="ngscstat_cov" value="ngsc_out.cov"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
450 <output name="stat_file" value="tx_stats.tabular"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
451 <output name="hist" value="hist.png" ftype="png" compare="sim_size"/>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
452 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
453 <!-- Calcuts -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
454 <test expect_num_outputs="2">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
455 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
456 <param name="functions" value="calcuts"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
457 <param name="input" value="test.stat"/>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
458 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
459 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
460 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
461 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
462 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
463 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
464 </section>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
465 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
466 <output name="calcuts_tab" value="calcuts_out.tsv"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
467 </test>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
468 <!-- Get seqs -->
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
469 <test expect_num_outputs="2">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
470 <conditional name="function_select">
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
471 <param name="functions" value="get_seqs"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
472 <param name="fasta_input" value="split_out.fasta"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
473 <param name="bed_input" value="dups.bed"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
474 <param name="coverage" value="-c"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
475 <param name="length" value="10"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
476 <param name="haplotigs" value="-a"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
477 <param name="min_ratio" value=".01"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
478 <param name="end_trim" value="-e"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
479 <param name="split" value="-s"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
480 <param name="min_gap" value="100000"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
481 </conditional>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
482 <output name="get_seqs_purged" value="purged_out.fa"/>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
483 </test>
3
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
484 <!-- pbcstat histogram options-->
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
485 <test expect_num_outputs="6">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
486 <conditional name="function_select">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
487 <param name="functions" value="pbcstat"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
488 <param name="input" value="test.paf"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
489 <param name="max_cov" value="1000"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
490 <param name="min_map_ratio" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
491 <param name="min_map_qual" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
492 <param name="flank" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
493 <param name="primary_alignments" value="-p"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
494 <section name="section_calcuts">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
495 <param name="min_depth" value="0.01"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
496 <param name="low_depth" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
497 <param name="transition" value="1"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
498 <param name="upper_depth" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
499 <param name="ploidy" value="-d 0"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
500 </section>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
501 <section name="section_hist">
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
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502 <param name="ymax" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
503 <param name="xmax" value="100"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
504 <param name="cutoffs_his" value="calcuts_out.tsv"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
505 </section>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
506 </conditional>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
507 <output name="calcuts_tab" value="calcuts_out.tsv"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
508 <output name="pbcstat_cov" value="out_hist_options.cov"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
509 <output name="pbcstat_wig" value="out_hist_options.wig"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
510 <output name="stat_file" value="pbcstats_hist_options.tabular"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
511 <output name="hist" value="hist_options.png" ftype="png" compare="sim_size"/>
76d4cbefff85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"
iuc
parents: 2
diff changeset
512 </test>
0
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
513 </tests>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
514 <help><![CDATA[
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
515 .. class:: infomark
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
516
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
517 **What it does**
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
518
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
519 The purge_dups tools are designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
520
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
521 ]]></help>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
522 <citations>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
diff changeset
523 <citation type="doi">10.1093/bioinformatics/btaa025</citation>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
parents:
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524 </citations>
8ec117da1796 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit ed3bf33e007841e359d164b2aa9e2ecf7fa5fa96"
iuc
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525 </tool>