Mercurial > repos > jjohnson > encyclopedia_fasta_to_prosit_csv

annotate encyclopedia_fasta_to_prosit_csv.xml @ 2:725e83e1eed1 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 6d8b020f1e4aefdb18a1642134ad551482a9f96f"
author jjohnson
date Wed, 01 Jul 2020 11:25:46 -0400
parents d0202c597434
children 91343296dbff
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d0202c597434 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
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1 <tool id="encyclopedia_fasta_to_prosit_csv" name="ConvertFastaToPrositCSV" version="@VERSION@.0" python_template_version="3.5">
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2 <description>Create Prosit CSV Input From a Protein FASTA</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 <command detect_errors="exit_code"><![CDATA[
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8 EncyclopeDIA -convert -fastatoprositcsv
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9 -i '$i'
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10 -minCharge $minCharge
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11 -maxCharge $maxCharge
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12 -defaultCharge $defaultCharge
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13 -maxMissedCleavage $maxMissedCleavage
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14 -minMz $minMz
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15 -maxMz $maxMz
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16 -defaultNCE $defaultNCE
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17 #if $enzyme
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18 -enzyme '$enzyme'
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19 #end if
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20 -o '$output'
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21 ]]></command>
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22 <inputs>
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23 <param argument="-i" type="data" format="fasta" label="Protein Fasta database"/>
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24 <param argument="-minCharge" type="integer" value="2" min="1" max="6" label="minCharge" help="(default: 2)"/>
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25 <param argument="-maxCharge" type="integer" value="3" min="1" max="6" label="maxCharge" help="(default: 3)"/>
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26 <param argument="-defaultCharge" type="integer" value="3" min="1" max="4" label="defaultCharge" help="(default: 3)"/>
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27 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="3" label="maxMissedCleavage" help="(default: 1)"/>
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28 <param argument="-minMz" type="float" value="396.4" min="150.0" max="1600.0" label="minMz" help="(default: 396.4)"/>
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29 <param argument="-maxMz" type="float" value="1002.7" min="150.0" max="1600.0" label="maxMz" help="(default: 1002.7)"/>
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30 <param argument="-defaultNCE" type="integer" value="33" min="25" max="40" label="Normalized Collision Energy" help="(default: 33)"/>
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31 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme" help="(default: Trypsin)">
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32 <option value="Trypsin">Trypsin</option>
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33 <option value="Lys-C">Lys-C</option>
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34 <option value="Lys-N">Lys-N</option>
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35 <option value="Arg-C">Arg-C</option>
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36 <option value="Glu-C">Glu-C</option>
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37 <option value="CNBr">CNBr</option>
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38 <option value="Chymotrypsin">Chymotrypsin</option>
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39 <option value="Pepsin A">Pepsin A</option>
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40 <option value="No Enzyme">No Enzyme</option>
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41 </param>
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42 </inputs>
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43 <outputs>
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44 <data name="output" format="csv" label="${i.name} Prosit_input.csv"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="i" ftype="fasta" value="YeastProteinFasta5.fasta"/>
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49 <output name="output" ftype="csv">
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50 <assert_contents>
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51 <has_text text="collision_energy"/>
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52 <has_text text="EDFFTVFDSLLR"/>
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 Create Prosit CSV From FASTA
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59 ]]></help>
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60 <expand macro="citations" />
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61 </tool>