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comparison netfilter.xml @ 0:0ce625cbce55 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc_tools/ucsc_netfilter commit 4babe88f84d0853e3a074fac19b62b457a59251b
author iuc
date Thu, 19 Sep 2024 06:23:38 +0000
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children 37da86f1f9e9
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-1:000000000000 0:0ce625cbce55
1 <tool id="ucsc_netfilter" name="netFilter" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
2 <description>
3 Filter out parts of net
4 </description>
5 <macros>
6 <token name="@TOOL_VERSION@">469</token>
7 </macros>
8 <xrefs>
9 <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
10 </xrefs>
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">ucsc-netfilter</requirement>
13 </requirements>
14 <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
15 <command detect_errors="exit_code"><![CDATA[
16 netFilter
17 '$in_net'
18 #if str($synteny.syn_filter) == "filtersyn"
19 $synteny.syntype
20 #if str($synteny.minSynScore)
21 -minSynScore=$synteny.minSynScore
22 #end if
23 #if str($synteny.minSynSize)
24 -minSynSize=$synteny.minSynSize
25 #end if
26 #if str($synteny.minSynAli)
27 -minSynAli=$synteny.minSynAli
28 #end if
29 #end if
30 #if str($minGap)
31 -minGap=$minGap
32 #end if
33 > '$out'
34 ]]></command>
35 <inputs>
36 <param name="in_net" format="ucsc.net" type="data" label="net dataset" help="" />
37
38 <conditional name="synteny">
39 <param name="syn_filter" type="select" label="Filter on synteny?">
40 <option value="skipsyn" selected="true">no</option>
41 <option value="filtersyn">yes</option>
42 </param>
43 <when value="skipsyn" />
44 <when value="filtersyn">
45 <param name="syntype" type="select" display="radio" label="Select synteny filter">
46 <option value="-syn" selected="true">filter on synteny tuned for human/mouse (-syn)</option>
47 <option value="-chimpSyn">filter on synteny tuned for human/chimp (-chimpSyn)</option>
48 <option value="-nonsyn">do inverse filtering based on synteny tuned for human/mouse (-nonsyn)</option>
49 </param>
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." />
51 <param argument="-minSynSize" type="integer" min="0" optional="true" label="Min syntenic block size" help="default 20,000" />
52 <param argument="-minSynAli" type="integer" min="0" optional="true" label="Min syntenic alignment size" help="default 10,000" />
53 </when>
54 </conditional>
55
56 <param argument="-minGap" type="integer" min="0" optional="true" label="Minimum gap" help="Restrict to those with gap size (tSize) >= minSize" />
57 </inputs>
58 <outputs>
59 <data name="out" format="ucsc.net" />
60 </outputs>
61 <tests>
62 <test expect_num_outputs="1">
63 <param name="in_net" value="in.ucsc.net" />
64 <conditional name="synteny">
65 <param name="syn_filter" value="filtersyn" />
66 <param name="syntype" value="-chimpSyn" />
67 </conditional>
68 <param name="minGap" value="300" />
69 <output name="out" file="out.ucsc.net" />
70 </test>
71 </tests>
72 <help><![CDATA[
73 **What it does**
74
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.
76
77 .. _netFilter: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
78 ]]> </help>
79 <citations>
80 <citation type="doi">10.1093/bib/bbs038</citation>
81 </citations>
82 </tool>