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comparison build_ucsc_custom_track.xml @ 2:3d87079756e1 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track commit 68ba77da2a1f8d6cd04dd7dc6efc5edcefcfa0c9"
author devteam
date Mon, 28 Feb 2022 20:06:04 +0000
parents 760f588e8a26
children
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1:760f588e8a26 2:3d87079756e1
1 <tool id="build_ucsc_custom_track_1" name="Build custom track" version="1.0.0"> 1 <tool id="build_ucsc_custom_track_1" name="Build custom track" version="1.0.1" profile="21.01">
2 <description>for UCSC genome browser</description> 2 <description>for UCSC genome browser</description>
3 <command interpreter="python"> 3 <requirements>
4 build_ucsc_custom_track.py 4 <requirement type="package" version="3.10">python</requirement>
5 "$out_file1" 5 </requirements>
6 #for $t in $tracks 6 <code file="build_ucsc_custom_track_code.py" />
7 "${t.input.file_name}" 7 <command detect_errors="exit_code"><![CDATA[
8 "${t.input.ext}" 8 python '$__tool_directory__/build_ucsc_custom_track.py'
9 #if $t.input.ext == "interval" 9 '$out_file1'
10 ${t.input.metadata.chromCol},${t.input.metadata.startCol},${t.input.metadata.endCol},${t.input.metadata.strandCol} 10 #for $t in $tracks
11 #else 11 '${t.input.file_name}'
12 "NA" 12 '${t.input.ext}'
13 #end if 13 #if $t.input.ext == "interval"
14 "${t.name}" 14 '${t.input.metadata.chromCol},${t.input.metadata.startCol},${t.input.metadata.endCol},${t.input.metadata.strandCol}'
15 "${t.description}" 15 #else
16 "${t.color}" 16 "NA"
17 "${t.visibility}" 17 #end if
18 #end for 18 '${t.name}'
19 </command> 19 '${t.description}'
20 <inputs> 20 "${t.color}"
21 <repeat name="tracks" title="Track"> 21 ${t.visibility}
22 <param name="input" type="data" format="interval,wig" label="Dataset"/> 22 #end for
23 <param name="name" type="text" value="User Track"> 23 ]]></command>
24 <validator type="length" max="15"/> 24 <inputs>
25 </param> 25 <repeat name="tracks" title="Track">
26 <param name="description" type="text" value="User Supplied Track (from Galaxy)"> 26 <param name="input" type="data" format="interval,wig" label="Dataset"/>
27 <validator type="length" max="60"/> 27 <param name="name" type="text" value="User Track">
28 </param> 28 <validator type="length" max="15"/>
29 <param label="Color" name="color" type="select"> 29 </param>
30 <option selected="yes" value="0-0-0">Black</option> 30 <param name="description" type="text" value="User Supplied Track (from Galaxy)">
31 <option value="255-0-0">Red</option> 31 <validator type="length" max="60"/>
32 <option value="0-255-0">Green</option> 32 </param>
33 <option value="0-0-255">Blue</option> 33 <param name="color" type="select" label="Color">
34 <option value="255-0-255">Magenta</option> 34 <option selected="yes" value="0-0-0">Black</option>
35 <option value="0-255-255">Cyan</option> 35 <option value="255-0-0">Red</option>
36 <option value="255-215-0">Gold</option> 36 <option value="0-255-0">Green</option>
37 <option value="160-32-240">Purple</option> 37 <option value="0-0-255">Blue</option>
38 <option value="255-140-0">Orange</option> 38 <option value="255-0-255">Magenta</option>
39 <option value="255-20-147">Pink</option> 39 <option value="0-255-255">Cyan</option>
40 <option value="92-51-23">Dark Chocolate</option> 40 <option value="255-215-0">Gold</option>
41 <option value="85-107-47">Olive green</option> 41 <option value="160-32-240">Purple</option>
42 </param> 42 <option value="255-140-0">Orange</option>
43 <param label="Visibility" name="visibility" type="select"> 43 <option value="255-20-147">Pink</option>
44 <option selected="yes" value="1">Dense</option> 44 <option value="92-51-23">Dark Chocolate</option>
45 <option value="2">Full</option> 45 <option value="85-107-47">Olive green</option>
46 <option value="3">Pack</option> 46 </param>
47 <option value="4">Squish</option> 47 <param name="visibility" type="select" label="Visibility">
48 <option value="0">Hide</option> 48 <option selected="yes" value="1">Dense</option>
49 </param> 49 <option value="2">Full</option>
50 </repeat> 50 <option value="3">Pack</option>
51 </inputs> 51 <option value="4">Squish</option>
52 <outputs> 52 <option value="0">Hide</option>
53 <data format="customtrack" name="out_file1" /> 53 </param>
54 </outputs> 54 </repeat>
55 </inputs>
56 <outputs>
57 <data name="out_file1" format="customtrack" />
58 </outputs>
55 <tests> 59 <tests>
56 <!--TODO: add a 2nd test here that includes 2 tracks --> 60 <!--TODO: add a 2nd test here that includes 2 tracks -->
57 <test> 61 <test>
58 <param name="input" value="customTrack1.bed" /> 62 <param name="input" value="customTrack1.bed" />
59 <param name="name" value="User Track" /> 63 <param name="name" value="User Track" />
60 <param name="description" value="User Supplied Track (from Galaxy)" /> 64 <param name="description" value="User Supplied Track (from Galaxy)" />
61 <param name="color" value="0-0-0" /> 65 <param name="color" value="0-0-0" />
62 <param name="visibility" value="1" /> 66 <param name="visibility" value="1" />
63 <output name="out_file1" file="build_ucsc_custom_track_out1.customtrack" /> 67 <output name="out_file1" file="build_ucsc_custom_track_out1.customtrack" />
64 </test> 68 </test>
65 </tests> 69 </tests>
66 <help> 70 <help><![CDATA[
67
68 .. class:: infomark 71 .. class:: infomark
69 72
70 This tool allows you to build custom tracks using datasets in your history for the UCSC genome browser. You can view these custom tracks on the UCSC genome browser by clicking on **display at UCSC main/test** link in the history panel of the output dataset. 73 This tool allows you to build custom tracks using datasets in your history for the UCSC genome browser. You can view these custom tracks on the UCSC genome browser by clicking on **display at UCSC main/test** link in the history panel of the output dataset.
71 74
72 ----- 75 -----
73 76
74 .. class:: warningmark 77 .. class:: warningmark
75 78
76 Please note that this tool requires **all input datasets(tracks) to have the same genome build**. The tool throws an error when this requirement is not met. You may then have to choose a valid dataset or remove invalid tracks. 79 Please note that this tool requires **all input datasets(tracks) to have the same genome build**. The tool throws an error when this requirement is not met. You may then have to choose a valid dataset or remove invalid tracks.
77 80 ]]></help>
78 </help>
79
80 <code file="build_ucsc_custom_track_code.py" />
81
82 </tool> 81 </tool>