annotate hicFindRestrictionSites.xml @ 5:3f552d62a93a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3e5c2f8ce3e540b0474746a33ee20b4a374dd38c"
author iuc
date Fri, 11 Dec 2020 21:44:35 +0000
parents 3c03ddb45833
children 8823a9d45ed0
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1 <tool id="hicexplorer_hicfindrestrictionsites" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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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>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @BINARY@
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10 --fasta '$fasta'
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11 --searchPattern '$searchPattern'
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12 --outFile restriction_site.bed
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14 ]]></command>
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15 <inputs>
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16 <param argument="--fasta" type="data" format='fasta'
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17 label="Fasta file for the organism genome."
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18 help="The organism genome fasta file to compute the restriction enzyme position."/>
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19 <param argument="--searchPattern" type="text" value=""
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20 label="Restriction enzyme sequence"
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21 help='Search pattern. For example, for HindIII this pattern is \"AAGCTT\".
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22 Both, forward and reverse strand are searched for a match. The pattern
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23 is a regexp and can contain regexp specif syntax
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24 (see https://docs.python.org/2/library/re.html). For example the pattern
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25 CG..GC will find all occurrence of CG followed by any two bases and then GC.'/>
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26 </inputs>
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27 <outputs>
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29 <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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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="fasta" value="hicFindRestrictionSites/reference_genome.fasta"/>
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36 <param name="searchPattern" value="GTAC"/>
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38 <output name="restrictionSites" file="hicFindRestrictionSites/restriction_sites.bed" ftype="bed" compare="sim_size"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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43 Find restriction sites
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44 ======================
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46 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.
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49 For more information about HiCExplorer please consider our documentation on readthedocs.io_
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51 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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52 ]]></help>
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53 <expand macro="citations" />
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54 </tool>