|
0
|
1 <tool id="bwtool-lift" name="bwtool-lift" version="1.0">
|
|
|
2 <description>Project data base-by-base into a new assembly using a liftOver chain file from UCSC</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package">bwtool</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command>
|
|
|
7 <![CDATA[
|
|
|
8 bwtool lift $in_bw $to_dbkey $out_bw
|
|
|
9 #if $unlifted.saveregions == "yes":
|
|
|
10 -unlifted=$unlifted.unlifted_file
|
|
|
11 #end if
|
|
|
12 #if $outwig.usetype == "yes":
|
|
|
13 -wigtype=$outwig.wigtype
|
|
|
14 #end if
|
|
|
15 $wigonly
|
|
|
16 #if $regions.useregions == "yes":
|
|
|
17 -regions=$regions.regionsbed
|
|
|
18 #end if
|
|
|
19 $condense
|
|
|
20 -decimals=$decimals
|
|
|
21 #if $fill.fillmissing == "yes":
|
|
|
22 -fill=$fill.fillvalue
|
|
|
23 #end if
|
|
|
24 -pseudo=$pseudo
|
|
|
25 ]]>
|
|
|
26 </command>
|
|
|
27 <inputs>
|
|
|
28 <param name="in_bw" type="data" format="bigwig" label="Convert coordinates of">
|
|
|
29 <param name="to_dbkey" type="select" label="To">
|
|
|
30 <options from_file="liftOver.loc">
|
|
|
31 <column name="name" index="1"/>
|
|
|
32 <column name="value" index="2"/>
|
|
|
33 <column name="dbkey" index="0"/>
|
|
|
34 <filter type="data_meta" ref="input" key="dbkey" column="0" />
|
|
|
35 </options>
|
|
|
36 </param>
|
|
|
37 <conditional name="outwig">
|
|
|
38 <param name="usetype" type="select" label="use specific regions?" help="">
|
|
|
39 <option value="no">no</option>
|
|
|
40 <option value="yes">yes</option>
|
|
|
41 </param>
|
|
|
42 <when value="no"/>
|
|
|
43 <when value="yes">
|
|
|
44 <param name="wigtype" type="select" label="Output type">
|
|
|
45 <option value="bg">bedGraph</option>
|
|
|
46 <option value="fix">fixedStep wig</option>
|
|
|
47 <option value="var">variableStep wig</option>
|
|
|
48 </param>
|
|
|
49 </when>
|
|
|
50 </conditional>
|
|
|
51 <param name="wigonly" type="boolean" truevalue="-wig-only" falsevalue="" checked="false"
|
|
|
52 label="wig-only"
|
|
|
53 help="for bigWig-creating programs, make a wig instead" />
|
|
|
54 <conditional name="regions">
|
|
|
55 <param name="useregions" type="select" label="use specific regions?" help="">
|
|
|
56 <option value="no">no</option>
|
|
|
57 <option value="yes">yes</option>
|
|
|
58 </param>
|
|
|
59 <when value="no"/>
|
|
|
60 <when value="yes">
|
|
|
61 <param name="regionsbed" type="data" format="bed" label="regions BED file"/>
|
|
|
62 </when>
|
|
|
63 </conditional>
|
|
|
64 <param name="regionsbed" type="data" format="bed" label="use specific regions"/>
|
|
|
65 <param name="condense" type="boolean" truevalue="-condense" falsevalue="" checked="true"
|
|
|
66 label="condense"
|
|
|
67 help="condense output, particularly bedGraphs" />
|
|
|
68 <conditional name="fillmissing">
|
|
|
69 <param name="fill" type="select" label="use specific regions?" help="">
|
|
|
70 <option value="no">no</option>
|
|
|
71 <option value="yes">yes</option>
|
|
|
72 </param>
|
|
|
73 <when value="no"/>
|
|
|
74 <when value="yes">
|
|
|
75 <param name="fillvalue" size="10" type="text" label="some programs allow filling missing parts of the bigWig with a specified value prior to using data"/>
|
|
|
76 </when>
|
|
|
77 </conditional>
|
|
|
78 <param name="fill" size="10" type="text" label="some programs allow filling missing parts of the bigWig with a specified value prior to using data"/>
|
|
|
79 <param name="pseudo" size="10" value="0" type="text" label="add a pseudo-count at every value"/>
|
|
|
80 </inputs>
|
|
|
81 <outputs>
|
|
|
82 <data format="txt" name="out_bw" label="${tool.name} result file on ${on_string}"/>
|
|
|
83 <conditional name="unlifted">
|
|
|
84 <param name="saveregions" type="select" label="Save all the regions from the input that are not lifted?" help="">
|
|
|
85 <option value="no">no</option>
|
|
|
86 <option value="yes">yes</option>
|
|
|
87 </param>
|
|
|
88 <when value="no"/>
|
|
|
89 <when value="yes">
|
|
|
90 <param name="unlifted_file" label="Unlifted regions on ${on_string}"/>
|
|
|
91 </when>
|
|
|
92 </conditional>
|
|
|
93 </outputs>
|
|
|
94 <help>
|
|
|
95 <![CDATA[
|
|
|
96
|
|
|
97 .. class:: infomark
|
|
|
98
|
|
|
99 **What it does**
|
|
|
100
|
|
|
101 The lift program does quite a useful thing when one needs to use data generated for an old genome assembly and doesn't necessarily have the time or the means to go through the steps of generating the equivalent data for a newer genome assembly. Lifting data is the process of converting the coordinates where that data lies, from one assembly to another through sequence alignment data. UCSC creates special alignment files for this purpose called liftOver chains and makes them available on their download page. Lifting is not a perfect process, but if the regions lifted are relatively short, usually only a small percent are not mappable through the chain. In the case of bigWig data, each base is mapped one by one, and is only mapped to the destination genome if it maps to a new locus unambiguously.
|
|
|
102
|
|
|
103
|
|
|
104 **Input**
|
|
|
105
|
|
|
106 Bigwig file
|
|
|
107
|
|
|
108
|
|
|
109 **References**
|
|
|
110
|
|
|
111
|
|
|
112 ]]>
|
|
|
113 </help>
|
|
|
114 </tool>
|
