annotate emboss_dan.xml @ 18:63dd26468588 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 18de4aa9ba00124b1b3e3afe14219e46931e58a9"
author iuc
date Fri, 09 Jul 2021 18:36:34 +0000
parents 8992d258e42f
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8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: dan19" name="dan" version="@VERSION@.1">
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2 <description>Calculates DNA RNA/DNA melting temperature</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <code file="emboss_format_corrector.py" />
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8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' dan -sequence '$input1' -windowsize $window -goutfile '$out_file1' -graph png -plot $plot1 -shiftincrement $shift -dnaconc $dnaconc
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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9 -saltconc $saltconc -product $product -formamide $formamide -mismatch $mismatch -prodlen $prodlen -thermo $thermo -temperature $temperature -rna $rna -outfile $out_file1 -auto</command>
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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10 <inputs>
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11 <param name="input1" type="data" format="data" label="On query" />
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12 <param name="window" type="integer" value="20" label="Window size" />
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13 <param name="shift" type="integer" value="1" label="Step size (shift increment)" />
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14 <param name="dnaconc" type="float" value="50.0" label="DNA Concentration (nM)" />
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15 <param name="saltconc" type="float" value="50.0" label="Salt concentration (mM)" />
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16 <param name="thermo" type="select" label="Output the DeltaG, DeltaH and DeltaS values">
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17 <option value="yes">Yes</option>
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18 <option value="no">No</option>
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19 </param>
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20 <param name="temperature" type="float" value="25.0" label="Temperature at which to calculate the DeltaG, DeltaH and DeltaS values" />
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21 <param name="rna" type="select" label="Sequence is RNA">
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22 <option value="no">No</option>
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23 <option value="yes">Yes</option>
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24 </param>
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25 <param name="product" type="select" label="Include percent formamide, percent of mismatches allowed and product length">
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26 <option value="no">No</option>
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27 <option value="yes">Yes</option>
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28 </param>
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29 <param name="formamide" type="float" value="0.0" label="Formamide concentration (nM)" />
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30 <param name="mismatch" type="float" value="0.0" label="Percent mismatch to be used in calculations" />
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31 <param name="prodlen" type="integer" value="20" label="Product length to be used in calculations" />
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32 <param name="plot1" type="select" label="Create a graph">
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33 <option value="no">No</option>
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34 <option value="yes">Yes</option>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data name="out_file1" format="dan" />
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39 </outputs>
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40 <!--
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41 <tests>
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42 <test>
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43 <param name="input1" value="2.fasta"/>
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44 <param name="window" value="20"/>
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45 <param name="shift" value="1"/>
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46 <param name="dnaconc" value="50"/>
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47 <param name="saltconc" value="50"/>
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48 <param name="thermo" value="yes"/>
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49 <param name="temperature" value="25"/>
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50 <param name="rna" value="no"/>
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51 <param name="product" value="no"/>
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52 <param name="formamide" value="0"/>
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53 <param name="mismatch" value="0"/>
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54 <param name="prodlen" value="20"/>
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55 <param name="plot1" value="yes"/>
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56 <output name="out_file1" file="emboss_dan_out.png"/>
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57 </test>
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58 </tests>
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59 -->
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60 <help>
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61 You can view the original documentation here_.
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62
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63 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/dan.html
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64 </help>
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65 <expand macro="citations" />
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66 </tool>