Mercurial > repos > bgruening > coprarna
annotate coprarna.xml @ 0:c580aaece010 draft default tip
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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| date | Wed, 01 Nov 2017 12:31:02 -0400 |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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1 <tool id="coprarna" name="coprarna" version="2.1.1"> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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2 <description> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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3 Phylogenetic target prediction for prokaryotic trans-acting small RNAs |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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4 </description> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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5 <requirements> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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6 <requirement type="package" version="2.1.1">coprarna</requirement> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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7 </requirements> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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8 <command detect_errors="aggressive"><![CDATA[ |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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9 CopraRNA2.pl |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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10 --srnaseq '$srnaseq' |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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11 --region '$region' |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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12 --ntup $ntup |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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13 --ntdown $ntdown |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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14 --rcsize $rcsize |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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15 --cores "\${GALAXY_SLOTS:-4}" |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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16 --winsize $winsize |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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17 --maxbpdist $maxbpdist |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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18 --cons $cons |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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19 --topcount $topcount |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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20 $cop1 |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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21 $nooi |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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22 --enrich $enrich |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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23 --root $root |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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24 ]]> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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25 </command> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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26 <inputs> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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27 <param name="srnaseq" type="data" format="fasta" label="FASTA file with small RNA sequences"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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28 <param name="region" type="select" label="Region to scan in whole genome target prediction." help="'5utr' for start codon, '3utr' for stop codon, 'cds' for entire transcript"> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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29 <option value="5utr" selected="true">5utr</option> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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30 <option value="3utr">3utr</option> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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31 <option value="cds">cds</option> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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32 </param> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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33 <param name="ntup" type="integer" value="200" label="Nucleotides upstream" help="Number of nucleotides upstream of 'region' to parse for targeting (def:200)" optional="true"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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34 <param name="ntdown" type="integer" value="100" label="Nucleotides downstream" help="Number of nucleotides downstream of '--region' to parse for targeting (def:100)" optional="true"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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35 <param name="rcsize" type="float" value="0.5" min="0" max="1" label="Fraction of putative target homologs" help="Minimum amount (%) of putative target homologs that need to be available for a target cluster to be considered in the CopraRNA1 part (see --cop1) of the prediction (def:0.5)"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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36 <param name="winsize" type="integer" value="150" label="Window size" help="IntaRNA target (--tAccW) window size parameter (def:150)" optional="true"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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37 <param name="maxbpdist" type="integer" value="100" label="Maximum basepair distance" help="IntaRNA target (--tAccL) maximum base pair distance parameter (def:100)" optional="true"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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38 <param name="cons" type="select" label="Controls consensus prediction" help="'0' for off, '1' for organism of interest based consensus, '2' for overall consensus based prediction"> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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39 <option value="0" selected="true">Off</option> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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40 <option value="1">Organism of interest based consensus</option> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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41 <option value="2">Overall consensus based prediction</option> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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42 </param> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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43 <param name="topcount" type="integer" value="200" label="Top predictions" help="Specifies the number of top predictions to return and use for the extended regions plots (def:200)" optional="true"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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44 <param name="cop1" truevalue="--cop1" falsevalue="" checked="False" type="boolean" label="CopraRNA1 prediction" help="Switch for CopraRNA1 prediction (def:off)"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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45 <param name="nooi" truevalue="--nooi" falsevalue="" checked="False" type="boolean" label="No focus on the organism of interest" help="If set then the CopraRNA2 prediction mode is set not to focus on the organism of interest (def:off)"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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46 <param name="enrich" type="integer" value="0" label="DAVID-WS functional enrichment" help="If set DAVID-WS functional enrichment is calculated with given number of top predictions (def:off)" optional="true"/> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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47 <param name="root" type="float" value="1" label="Root function" help="Specifies root function to apply to the weights (def:1)"/> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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48 </inputs> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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49 <outputs> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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50 <data format="csv" name="result" from_work_dir="./CopraRNA_result.csv" label="CopraRNA result csv"/> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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51 <data format="pdf" name="conservationheatmap" from_work_dir="./sRNA_conservation_heatmap.pdf" label="sRNA conservation heatmap"/> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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52 <data format="pdf" name="functionheatmap" from_work_dir="./Enrichment/enriched_heatmap_big.pdf" label="Functional enrichment heatmap"/> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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53 </outputs> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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54 <tests> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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55 <test expect_exit_code="1" expect_failure="true"> |
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c580aaece010
planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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56 <param name="srnaseq" value="copra.fa"/> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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57 <assert_stderr> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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58 <has_text text="Error: The input file" /> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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59 </assert_stderr> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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60 </test> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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61 </tests> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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62 <help> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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63 <![CDATA[ |
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64 |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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65 **What it does** |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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66 |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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67 Phylogenetic target prediction for prokaryotic trans-acting small RNAs |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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68 |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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69 CopraRNA is a tool for sRNA target prediction. It computes whole genome target predictions by combination of distinct whole genome IntaRNA predictions. As input CopraRNA requires at least 3 homologous sRNA sequences from 3 distinct organisms in FASTA format. Furthermore, each organisms' genome has to be part of the NCBI Reference Sequence (RefSeq) database (i.e. it should have exactly this NZ_* or this NC_XXXXXX format where * stands for any character and X stands for a digit between 0 and 9). Depending on sequence length (target and sRNA), amount of input organisms and genome sizes, CopraRNA can take up to 24h or longer to compute. In most cases it is significantly faster. |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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70 |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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71 **Output** |
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72 List of conserved identified interactions |
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73 |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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74 ]]> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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75 |
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76 </help> |
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planemo upload for repository https://github.com/PatrickRWright/CopraRNA commit c555b71250ec51e75bb250d9d8d155bc9878390a
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77 <citations> |
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78 <citation type="doi">10.1093/nar/gku359</citation> |
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79 </citations> |
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80 </tool> |