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comparison hicup_digester.xml @ 0:d0bfaeca5e25 draft default tip

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
author bgruening
date Thu, 09 Mar 2017 08:31:45 -0500
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1 <tool id="hicup_digester" name="Hicup Digester" version="0.1.0">
2 <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
3 <macros>
4 <import>hicup_macros.xml</import>
5 </macros>
6 <expand macro="requirements_hicup" />
7 <expand macro="stdio" />
8
9 <command><![CDATA[
10 hicup_digester --re1 '$re1' --genome '$genome'
11 #if $advanced_options.re2:
12 --re2 '$advanced_options.re2'
13 #end if
14 #for $file in $input_files_digest:
15 $file
16 #end for
17 && mv *Digest_* digester_file.txt
18 ]]></command>
19 <inputs>
20 <expand macro="digester_input" />
21 <expand macro="re1" />
22 <section name="advanced_options" title="Advanced options">
23 <expand macro="re2" />
24 </section>
25 </inputs>
26 <outputs>
27 <data name="digest_file" format="txt" from_work_dir="digester_file.txt" label="Digester File.txt"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="input_files_digest" value="chr1.fa"/>
32 <param name="re1" value="A^AGCTT"/>
33 <param name="genome" value="human"/>
34 <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
35 </test>
36 </tests>
37 <help><![CDATA[
38
39 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
40
41 To get more information about the digister visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Digester
42 ]]></help>
43 <expand macro="citation_hicup" />
44 </tool>