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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit 2c48ae5db2dd1508970cc4545cbdfb77bc010eba
author bgruening
date Wed, 13 Mar 2024 10:22:43 +0000
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2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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1 <tool id="Nucleosome" name="Nucleosome Predictions" version="3.0">
1
49d81e777389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit 2c48ae5db2dd1508970cc4545cbdfb77bc010eba
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2 <xrefs>
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3 <xref type="bio.tools">nucleosome_prediction</xref>
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4 </xrefs>
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5 <requirements>
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6 <requirement type="package" version="3.0">nucleosome_prediction</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 nucleosome_prediction.pl
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10 -t Example
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11 -s '$input'
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12 -p predition_output
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13 -tab
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14 -c $c
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15 -temp $temp
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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16 $raw_binding
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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17 ]]></command>
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18
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19 <inputs>
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20 <param type="data" name="input" label="Input sequence file (.fasta format)" format="fasta" />
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21 <param argument="-c" type="float" value="0.1"
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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22 label="Nucleosomes Concentration" help="Nucleosomes concentration: the default value = 0.1"/>
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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23 <param argument="-temp" type="integer" value="1"
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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24 label="Temperature Scaling" help="Temperature scaling: the default value = 1"/>
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25 <param argument="-raw_binding" type="boolean" truevalue="-raw_binding" falsevalue=""
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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26 label="Raw Binding" help="Raw Binding: When 'No' (default), then the output will be the default average occupancy probabilities. When 'yes', then the output will be the raw nucleosome binding log-ratio per basepair"/>
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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27 </inputs>
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28
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29 <outputs>
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30 <data name="output" format="tabular" from_work_dir="predition_output.tab" />
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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31 </outputs>
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32
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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33 <tests>
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34 <test>
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35 <param name="input" value="input.fa" ftype="fasta"/>
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36 <param name="raw_binding" value="True"/>
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37 <output name="output" file="npresults.tab" ftype="tabular"/>
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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38 </test>
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39 <test>
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40 <param name="input" value="input.fa" ftype="fasta"/>
2c42bb973ac3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction commit b309226826df04a53a14b1867547ce6c4810648f
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41 <param name="c" value="0.1"/>
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42 <param name="temp" value="1"/>
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43 <output name="output" file="npresultsf.tab" ftype="tabular"/>
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44 </test>
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45 </tests>
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46
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47 <help><![CDATA[
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48
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49 **What it does**
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50 This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers:
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51 This version (version 3) is applicable to all species.
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52
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53 The tool takes a sequence .fasta file and finds all positions of the matrices above the background
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54
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55 ]]></help>
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56
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57 <citations>
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58
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59 <citation type="bibtex">
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60 @MISC{10.1038/nature07667,
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61 DOI = {10.1038/nature07667},
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62 note = {The DNA-encoded nucleosome organization of a eukaryotic genome}
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63 year = "2009"
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64 }
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65 </citation>
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66 </citations>
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67
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68 </tool>