Mercurial > repos > bgruening > hicexplorer_hicfindrestrictionsites
comparison hicFindRestrictionSites.xml @ 6:8823a9d45ed0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author | iuc |
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date | Tue, 16 Mar 2021 14:51:57 +0000 |
parents | 3c03ddb45833 |
children | 9369e9b11b8d |
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5:3f552d62a93a | 6:8823a9d45ed0 |
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1 <tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | 1 <tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
2 <description>identify restriction enzyme sites</description> | 2 <description>identify restriction enzyme sites</description> |
3 <macros> | 3 <macros> |
4 <token name="@BINARY@">hicFindRestSite</token> | 4 <token name="@BINARY@">hicFindRestSite</token> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
9 @BINARY@ | 9 @BINARY@ |
10 --fasta '$fasta' | 10 --fasta '$fasta' |
11 --searchPattern '$searchPattern' | 11 --searchPattern '$searchPattern' |
12 --outFile restriction_site.bed | 12 --outFile restriction_site.bed |
13 | 13 |
14 ]]></command> | 14 ]]> </command> |
15 <inputs> | 15 <inputs> |
16 <param argument="--fasta" type="data" format='fasta' | 16 <param argument="--fasta" type="data" format='fasta,fasta.gz' label="Fasta file for the organism genome." help="The organism genome fasta file to compute the restriction enzyme position." /> |
17 label="Fasta file for the organism genome." | 17 <param argument="--searchPattern" type="text" value="" label="Restriction enzyme sequence" help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\". |
18 help="The organism genome fasta file to compute the restriction enzyme position."/> | |
19 <param argument="--searchPattern" type="text" value="" | |
20 label="Restriction enzyme sequence" | |
21 help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\". | |
22 Both, forward and reverse strand are searched for a match. The pattern | 18 Both, forward and reverse strand are searched for a match. The pattern |
23 is a regexp and can contain regexp specif syntax | 19 is a regexp and can contain regexp specif syntax |
24 (see https://docs.python.org/2/library/re.html). For example the pattern | 20 (see https://docs.python.org/2/library/re.html). For example the pattern |
25 CG..GC will find all occurrence of CG followed by any two bases and then GC.'/> | 21 CG..GC will find all occurrence of CG followed by any two bases and then GC.'> |
22 <validator type="expression" message="Only ASCII characters are allowed.">value.isascii()</validator> | |
23 </param> | |
26 </inputs> | 24 </inputs> |
27 <outputs> | 25 <outputs> |
28 | 26 <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites" /> |
29 <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites"/> | |
30 | |
31 </outputs> | 27 </outputs> |
32 <tests> | 28 <tests> |
33 <test> | 29 <test> |
34 <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta"/> | 30 <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta" /> |
35 | 31 <param name="searchPattern" value="GTAC" /> |
36 <param name="searchPattern" value="GTAC"/> | 32 <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" /> |
37 | |
38 <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" compare="sim_size"/> | |
39 </test> | 33 </test> |
40 </tests> | 34 </tests> |
41 <help><![CDATA[ | 35 <help><![CDATA[ |
42 | 36 |
43 Find restriction sites | 37 Find restriction sites |
47 | 41 |
48 | 42 |
49 For more information about HiCExplorer please consider our documentation on readthedocs.io_ | 43 For more information about HiCExplorer please consider our documentation on readthedocs.io_ |
50 | 44 |
51 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | 45 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html |
52 ]]></help> | 46 ]]> </help> |
53 <expand macro="citations" /> | 47 <expand macro="citations" /> |
54 </tool> | 48 </tool> |