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comparison pretext_graph.xml @ 0:716ec61855a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08
author iuc
date Mon, 28 Oct 2024 09:15:11 +0000
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children 204c10e3703c
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-1:000000000000 0:716ec61855a1
1 <tool id="pretext_graph" name="Pretextgraph" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>Embed bedgraph formatted data inside a Pretext contact map.</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.0.6</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">pretextgraph</requirement>
9 <requirement type="package" version="377"> ucsc-bigwigtobedgraph</requirement>
10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[
12 cp '$pretext' input.pretext &&
13 #if $input.is_of_type("bedgraph"):
14 cat '$input' |
15 #else if $input.is_of_type("bigwig"):
16 ln -s '$input' input.bigwig &&
17 bigWigToBedGraph input.bigwig /dev/stdout |
18 #end if
19 PretextGraph -i input.pretext
20 #if $name:
21 -n '$name'
22 #end if
23 -o output.pretext
24 ]]></command>
25 <inputs>
26 <param name="input" type="data" format="bigwig,bedgraph" label="Input bigwig or bedgraph file"/>
27 <param name="pretext" type="data" format="pretext" label="Pretext file" help="Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant."/>
28 <param name="name" type="text" label="Label for the graph" optional="true"/>
29 </inputs>
30 <outputs>
31 <data name="graph_out" format="pretext" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
32 </outputs>
33 <tests>
34 <!-- BIGWIG TEST -->
35 <test expect_num_outputs="1">
36 <param name="input" value="input_graph.bw" ftype="bigwig"/>
37 <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
38 <param name="name" value="testing"/>
39 <output name="graph_out" file="output_4.pretext"/>
40 </test>
41 <!-- BEDGRAPH TEST -->
42 <test expect_num_outputs="1">
43 <param name="input" value="input_graph.bgr" ftype="bedgraph"/>
44 <param name="pretext" value="input_graph.pretext" ftype="pretext"/>
45 <param name="name" value="testing_2"/>
46 <output name="graph_out" file="output_5.pretext"/>
47 </test>
48 </tests>
49 <help><![CDATA[
50 Adds additional data onto existing pretextmap files.
51 Input Pretext file acts as a foundation for additional data to be added onto.
52 Sequence names in the Pretext file must match sequence names in the bedgraph data; although relative sort order is unimportant.
53 The chosen name acts as a lable on the graph.
54 ]]></help>
55 <citations>
56 <citation type="bibtex">
57 @misc{Harry_et_al,
58 Author={Harry, E},
59 title={Paired REad TEXTure Graph: Embeds bedgraph data into Pretext contact maps.},
60 url = {https://github.com/wtsi-hpag/PretextGraph},}
61 </citation>
62 </citations>
63 </tool>