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annotate hicFindRestrictionSites.xml @ 6:9cbb4e6ce509 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 45892bbb7b760b9d35299ed50028d4c5c5741970"
author iuc
date Thu, 08 Apr 2021 19:43:47 +0000
parents b7ce646b29e1
children 00174edbfdaa
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b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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1 <tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>identify restriction enzyme sites</description>
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3 <macros>
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4 <token name="@BINARY@">hicFindRestSite</token>
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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5 <import>macros.xml</import>
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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6 </macros>
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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7 <expand macro="requirements" />
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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8 <command detect_errors="exit_code"><![CDATA[
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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9 @BINARY@
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10 --fasta '$fasta'
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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11 --searchPattern '$searchPattern'
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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12 --outFile restriction_site.bed
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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14 ]]> </command>
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5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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15 <inputs>
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b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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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." />
b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
iuc
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17 <param argument="--searchPattern" type="text" value="" label="Restriction enzyme sequence" help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\".
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c389a701161e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
iuc
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18 Both, forward and reverse strand are searched for a match. The pattern
c389a701161e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
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19 is a regexp and can contain regexp specif syntax
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20 (see https://docs.python.org/2/library/re.html). For example the pattern
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b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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21 CG..GC will find all occurrence of CG followed by any two bases and then GC.'>
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9cbb4e6ce509 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 45892bbb7b760b9d35299ed50028d4c5c5741970"
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22 <validator type="expression" message="Only ASCII characters are allowed."><![CDATA[all(ord(c) < 128 for c in value)]]></validator>
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b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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23 </param>
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5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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24 </inputs>
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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25 <outputs>
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26 <data name="restrictionSites" from_work_dir="restriction_site.bed" format="bed" label="${tool.name} on ${fasta.name} ${searchPattern} [${on_string}]: Restriction sites" />
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5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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27 </outputs>
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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28 <tests>
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29 <test>
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b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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30 <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta" />
b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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31 <param name="searchPattern" value="GTAC" />
b7ce646b29e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
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32 <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" />
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5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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33 </test>
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34 </tests>
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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35 <help><![CDATA[
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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37 Find restriction sites
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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38 ======================
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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40 This scripts find the locations of a given restriction enzyme sequence. This file can be used to build an Hi-C interaction matrix with restriction enzyme resolution by hicBuildMatrix.
5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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5c62f55474fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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43 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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45 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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46 ]]> </help>
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47 <expand macro="citations" />
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48 </tool>