Mercurial > repos > iuc > ucsc_netfilter

annotate netfilter.xml @ 1:37da86f1f9e9 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter commit 303002db06287fb25306020c4391626842f52162
author iuc
date Sun, 22 Sep 2024 07:25:46 +0000
parents 0ce625cbce55
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0ce625cbce55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter commit 4babe88f84d0853e3a074fac19b62b457a59251b
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1 <tool id="ucsc_netfilter" name="netFilter" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
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2 <description>
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3 Filter out parts of net
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4 </description>
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5 <macros>
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6 <token name="@TOOL_VERSION@">469</token>
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7 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
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10 </xrefs>
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">ucsc-netfilter</requirement>
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13 </requirements>
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14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
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15 <command detect_errors="exit_code"><![CDATA[
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16 netFilter
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17 '$in_net'
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18 #if str($synteny.syn_filter) == "filtersyn"
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19 $synteny.syntype
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20 #if str($synteny.minSynScore)
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21 -minSynScore=$synteny.minSynScore
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22 #end if
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23 #if str($synteny.minSynSize)
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24 -minSynSize=$synteny.minSynSize
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25 #end if
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26 #if str($synteny.minSynAli)
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27 -minSynAli=$synteny.minSynAli
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28 #end if
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29 #end if
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30 #if str($minGap)
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31 -minGap=$minGap
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32 #end if
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33 > '$out'
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34 ]]></command>
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35 <inputs>
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36 <param name="in_net" format="ucsc.net" type="data" label="net dataset" help="" />
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37
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38 <conditional name="synteny">
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39 <param name="syn_filter" type="select" label="Filter on synteny?">
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40 <option value="skipsyn" selected="true">no</option>
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41 <option value="filtersyn">yes</option>
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42 </param>
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43 <when value="skipsyn" />
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44 <when value="filtersyn">
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45 <param name="syntype" type="select" display="radio" label="Select synteny filter">
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46 <option value="-syn" selected="true">filter on synteny tuned for human/mouse (-syn)</option>
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47 <option value="-chimpSyn">filter on synteny tuned for human/chimp (-chimpSyn)</option>
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48 <option value="-nonsyn">do inverse filtering based on synteny tuned for human/mouse (-nonsyn)</option>
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49 </param>
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50 <param argument="-minSynScore" type="integer" optional="true" label="Min syntenic block score" help="default 200,000: covers 27,000 bases including 9,000 aligning--a very stringent requirement." />
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51 <param argument="-minSynSize" type="integer" min="0" optional="true" label="Min syntenic block size" help="default 20,000" />
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52 <param argument="-minSynAli" type="integer" min="0" optional="true" label="Min syntenic alignment size" help="default 10,000" />
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53 </when>
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54 </conditional>
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55
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56 <param argument="-minGap" type="integer" min="0" optional="true" label="Minimum gap" help="Restrict to those with gap size (tSize) >= minSize" />
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57 </inputs>
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58 <outputs>
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59 <data name="out" format="ucsc.net" />
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60 </outputs>
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61 <tests>
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62 <test expect_num_outputs="1">
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63 <param name="in_net" value="in.ucsc.net" />
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64 <conditional name="synteny">
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65 <param name="syn_filter" value="filtersyn" />
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66 <param name="syntype" value="-chimpSyn" />
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67 </conditional>
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68 <param name="minGap" value="300" />
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69 <output name="out" file="out.ucsc.net" />
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 **What it does**
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74
1
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75 `netFilter`_ is a tool to filter out parts of `net`_. What passes filter goes to output. Note a net is a recursive data structure. If a parent fails to pass the filter, the children are not even considered.
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76
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77 For implementation details see netFilter's `source code`_.
0
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78
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79 .. _netFilter: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
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80 .. _net: https://genome.ucsc.edu/goldenPath/help/net.html
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81 .. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/netFilter/netFilter.c
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82 ]]> </help>
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83 <citations>
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84 <citation type="doi">10.1093/bib/bbs038</citation>
0ce625cbce55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter commit 4babe88f84d0853e3a074fac19b62b457a59251b
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85 </citations>
0ce625cbce55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter commit 4babe88f84d0853e3a074fac19b62b457a59251b
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86 </tool>