Mercurial > repos > iuc > crossmap_wig

annotate crossmap_wig.xml @ 2:f36c2d58e591 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
author iuc
date Thu, 19 Oct 2017 12:39:22 -0400
parents 0d0d8d882315
children 792bd038a59c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
1 <tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@-0">
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
3 <macros>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
4 <import>macros.xml</import>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
5 </macros>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
6 <expand macro="requirements"/>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
7 <expand macro="stdio"/>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
8 <expand macro="version_command"/>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
9 <command><![CDATA[
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
10 CrossMap.py wig
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
11 '${chain_source.input_chain}'
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
12 '${input}'
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
13 '${output}'
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
14
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
15 && mv '${output}.bw' '${output}'
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
16 && mv '${output}.sorted.bgr' '${output2}'
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
17 ]]></command>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
18
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
19 <inputs>
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
20 <param name="input" type="data" format="wig" label="Wiggle file"/>
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
21
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
22 <expand macro="chain" />
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
23 </inputs>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
24
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
25 <outputs>
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
26 <data name="output" format="wig" label="${tool.name} on ${on_string}" />
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
27 <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" />
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
28 </outputs>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
29
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
30 <tests>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
31 <!-- WIG - Doesn't understand fixedStep -->
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
32 <test>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
33 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
34 <param name="index_source" value="history"/>
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
35 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
36
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
37 <output name="output" file="test_wig_01_output_a.bw"/>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
38 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
39 </test>
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
40
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
41 <test>
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
42 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
43 <param name="index_source" value="cached"/>
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
44
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
45 <output name="output" file="test_wig_01_output_a.bw"/>
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
46 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
47 </test>
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
48 </tests>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
49 <help><![CDATA[
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
50 @HELP_GENERAL@
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
51
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
52 Wig
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
53 ---
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
54
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
55 Input wiggle data can be in variableStep (for data with irregular
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
56 intervals) or fixedStep (for data with regular intervals). Regardless of
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
57 the input, the output will always in bedGraph format. bedGraph format is
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
58 similar to wiggle format and can be converted into BigWig format using UCSC
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
59 wigToBigWig tool. We export files in bedGraph because it is usually much
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
60 smaller than file in wiggle format, and more importantly, CrossMap
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
61 internally transforms wiggle into bedGraph to increase running speed.
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
62
2
f36c2d58e591 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 93bc570011b7cad70abf36695823478f819b81f1
iuc
parents: 0
diff changeset
63 ]]></help>
0
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
64
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
65 <citations>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
66 <citation type="doi">10.1093/bioinformatics/btt730</citation>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
67 </citations>
0d0d8d882315 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 8564863eaad7bb9f9c8c273d471511979a2c96aa
iuc
parents:
diff changeset
68 </tool>