Mercurial > repos > iuc > circos
annotate stack-histogram.xml @ 11:31a35811dda6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"
author | iuc |
---|---|
date | Tue, 16 Nov 2021 09:20:08 +0000 |
parents | df7356989ac1 |
children | c4bde687c846 |
rev | line source |
---|---|
6
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
2 <tool id="circos_wiggle_to_stacked" name="Circos: Stack bigWigs as Histogram" version="@WRAPPER_VERSION@"> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
3 <description>reformats for use in Circos stacked histogram plots</description> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
4 <macros> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
5 <import>macros.xml</import> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
6 </macros> |
9
df7356989ac1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
iuc
parents:
6
diff
changeset
|
7 <edam_topics> |
df7356989ac1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
iuc
parents:
6
diff
changeset
|
8 <edam_topic>topic_0797</edam_topic> |
df7356989ac1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
iuc
parents:
6
diff
changeset
|
9 <edam_topic>topic_0092</edam_topic> |
df7356989ac1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
iuc
parents:
6
diff
changeset
|
10 </edam_topics> |
df7356989ac1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
iuc
parents:
6
diff
changeset
|
11 <edam_operations> |
df7356989ac1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
iuc
parents:
6
diff
changeset
|
12 <edam_operation>operation_0335</edam_operation> |
df7356989ac1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 041a4d1618298f540e3917f00781e09ec7d71b75"
iuc
parents:
6
diff
changeset
|
13 </edam_operations> |
11
31a35811dda6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit b9ec351920dbc83fa14bd1f8cfdd0a6a19b89473"
iuc
parents:
9
diff
changeset
|
14 <expand macro="requirements" /> |
6
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
15 <command detect_errors="exit_code"><![CDATA[ |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
16 python |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
17 '$__tool_directory__/stack-histogram.py' |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
18 #for i in $input |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
19 '$i' |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
20 #end for |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
21 > '$output' |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
22 ]]></command> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
23 <inputs> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
24 <param name="input" type="data" format="bigwig" label="BigWig files" multiple="True" help="These MUST have identical chromosomes and intervals, within their datasets. This tool is incredibly, intentionally naïve, and will crash if there are missing ranges in some bigwig files. This feels like a reasonable assumption to make (simplifies processing) at the expense of theoretical correctness, given that when you are stacking histograms they're probably coming from the same upstream pipeline with the same settings (i.e. step/width/etc.)"/> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
25 </inputs> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
26 <outputs> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
27 <data name="output" format="tabular" /> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
28 </outputs> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
29 <tests> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
30 <test> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
31 <param name="input" value="scatter/1.bw,scatter/1.bw,scatter/1.bw" ftype="bigwig" /> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
32 <output name="output" file="scatter/1.multi.out" ftype="tabular" /> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
33 </test> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
34 </tests> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
35 <help><![CDATA[ |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
36 Converts standard bigWig files into a format appropriate for Circos stacked histogram plots |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
37 |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
38 If you need to process bedgraph, please convert those to bigwig first. |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
39 ]]></help> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
40 <expand macro="citations" /> |
740057a5126d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circos commit 1584882716a1d2c598e8485da9d73bcf80d9b29a"
iuc
parents:
diff
changeset
|
41 </tool> |