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comparison coverage.xml @ 3:4ef9819dc7fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/coverage commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:02 -0400
parents 16b62a897aac
children e3363e087468
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2:bc9c66c1e9c9 3:4ef9819dc7fb
1 <tool id="gops_coverage_1" name="Coverage" version="1.0.0"> 1 <tool id="gops_coverage_1" name="Coverage" version="1.0.0">
2 <description>of a set of intervals on second set of intervals</description> 2 <description>of a set of intervals on second set of intervals</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.7.1">bx-python</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> 5 </macros>
6 </requirements> 6 <expand macro="requirements" />
7 <command interpreter="python">gops_coverage.py $input1 $input2 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}</command> 7 <code file="operation_filter.py"/>
8 <inputs> 8 <command><![CDATA[
9 <param format="interval" name="input1" type="data" help="First dataset"> 9 python '$__tool_directory__/gops_coverage.py'
10 <label>What portion of</label> 10 '$input1'
11 </param> 11 '$input2'
12 <param format="interval" name="input2" type="data" help="Second dataset"> 12 '$output'
13 <label>is covered by</label> 13 -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}
14 </param> 14 -2 ${input2.metadata.chromCol},${input2.metadata.startCol},${input2.metadata.endCol},${input2.metadata.strandCol}
15 </inputs> 15 ]]></command>
16 <outputs> 16 <inputs>
17 <data format="interval" name="output" metadata_source="input1" /> 17 <param name="input1" type="data" format="interval" label="What portion of" help="First dataset" />
18 </outputs> 18 <param name="input2" type="data" format="interval" label="Is covered by" help="Second dataset" />
19 <code file="operation_filter.py"/> 19 </inputs>
20 <tests> 20 <outputs>
21 <test> 21 <data name="output" format_source="input1" metadata_source="input1" />
22 <param name="input1" value="1.bed" /> 22 </outputs>
23 <param name="input2" value="2.bed" /> 23 <tests>
24 <output name="output" file="gops_coverage_out.interval" /> 24 <test>
25 </test> 25 <param name="input1" value="1.bed" />
26 <test> 26 <param name="input2" value="2.bed" />
27 <param name="input1" value="1.bed" /> 27 <output name="output" file="gops_coverage_out.interval" />
28 <param name="input2" value="2_mod.bed" ftype="interval"/> 28 </test>
29 <output name="output" file="gops_coverage_out_diffCols.interval" /> 29 <test>
30 </test> 30 <param name="input1" value="1.bed" />
31 <test> 31 <param name="input2" value="2_mod.bed" ftype="interval"/>
32 <param name="input1" value="gops_bigint.interval" /> 32 <output name="output" file="gops_coverage_out_diffCols.interval" />
33 <param name="input2" value="gops_bigint2.interval" /> 33 </test>
34 <output name="output" file="gops_coverage_out2.interval" /> 34 <test>
35 </test> 35 <param name="input1" value="gops_bigint.interval" />
36 </tests> 36 <param name="input2" value="gops_bigint2.interval" />
37 <help> 37 <output name="output" file="gops_coverage_out2.interval" />
38 38 </test>
39 </tests>
40 <help><![CDATA[
39 .. class:: infomark 41 .. class:: infomark
40 42
41 **TIP:** If your dataset does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. 43 **TIP:** If your dataset does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns.
42 44
43 Find the coverage of intervals in the first dataset on intervals in the second dataset. The coverage is added as two columns, the first being bases covered, and the second being the fraction of bases covered by that interval. 45 Find the coverage of intervals in the first dataset on intervals in the second dataset. The coverage is added as two columns, the first being bases covered, and the second being the fraction of bases covered by that interval.
44 46
45 ----- 47 @SCREENCASTS@
46
47 **Screencasts!**
48
49 See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
50
51 .. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
52
53 -----
54 48
55 **Example** 49 **Example**
56
57 50
58 if **First dataset** are genes :: 51 if **First dataset** are genes ::
59 52
60 chr11 5203271 5204877 NM_000518 0 - 53 chr11 5203271 5204877 NM_000518 0 -
61 chr11 5210634 5212434 NM_000519 0 - 54 chr11 5210634 5212434 NM_000519 0 -
88 For example, the following line of output:: 81 For example, the following line of output::
89 82
90 chr11 5203271 5204877 NM_000518 0 - 172 0.107098 83 chr11 5203271 5204877 NM_000518 0 - 172 0.107098
91 84
92 implies that 172 nucleotides accounting for 10.7% of the this interval (chr11:5203271-5204877) overlap with repetitive elements. 85 implies that 172 nucleotides accounting for 10.7% of the this interval (chr11:5203271-5204877) overlap with repetitive elements.
93 86 ]]></help>
94 </help>
95 </tool> 87 </tool>