Mercurial > repos > jjohnson > encyclopedia_fasta_to_prosit_csv
diff encyclopedia_fasta_to_prosit_csv.xml @ 0:d0202c597434 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author | jjohnson |
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date | Fri, 19 Jun 2020 10:21:58 -0400 |
parents | |
children | 91343296dbff |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/encyclopedia_fasta_to_prosit_csv.xml Fri Jun 19 10:21:58 2020 -0400 @@ -0,0 +1,61 @@ +<tool id="encyclopedia_fasta_to_prosit_csv" name="ConvertFastaToPrositCSV" version="@VERSION@.0" python_template_version="3.5"> + <description>Create Prosit CSV Input From a Protein FASTA</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + EncyclopeDIA -convert -fastatoprositcsv + -i '$i' + -minCharge $minCharge + -maxCharge $maxCharge + -defaultCharge $defaultCharge + -maxMissedCleavage $maxMissedCleavage + -minMz $minMz + -maxMz $maxMz + -defaultNCE $defaultNCE + #if $enzyme + -enzyme '$enzyme' + #end if + -o '$output' + ]]></command> + <inputs> + <param argument="-i" type="data" format="fasta" label="Protein Fasta database"/> + <param argument="-minCharge" type="integer" value="2" min="1" max="6" label="minCharge" help="(default: 2)"/> + <param argument="-maxCharge" type="integer" value="3" min="1" max="6" label="maxCharge" help="(default: 3)"/> + <param argument="-defaultCharge" type="integer" value="3" min="1" max="4" label="defaultCharge" help="(default: 3)"/> + <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="3" label="maxMissedCleavage" help="(default: 1)"/> + <param argument="-minMz" type="float" value="396.4" min="150.0" max="1600.0" label="minMz" help="(default: 396.4)"/> + <param argument="-maxMz" type="float" value="1002.7" min="150.0" max="1600.0" label="maxMz" help="(default: 1002.7)"/> + <param argument="-defaultNCE" type="integer" value="33" min="25" max="40" label="Normalized Collision Energy" help="(default: 33)"/> + <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme" help="(default: Trypsin)"> + <option value="Trypsin">Trypsin</option> + <option value="Lys-C">Lys-C</option> + <option value="Lys-N">Lys-N</option> + <option value="Arg-C">Arg-C</option> + <option value="Glu-C">Glu-C</option> + <option value="CNBr">CNBr</option> + <option value="Chymotrypsin">Chymotrypsin</option> + <option value="Pepsin A">Pepsin A</option> + <option value="No Enzyme">No Enzyme</option> + </param> + </inputs> + <outputs> + <data name="output" format="csv" label="${i.name} Prosit_input.csv"/> + </outputs> + <tests> + <test> + <param name="i" ftype="fasta" value="YeastProteinFasta5.fasta"/> + <output name="output" ftype="csv"> + <assert_contents> + <has_text text="collision_energy"/> + <has_text text="EDFFTVFDSLLR"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Create Prosit CSV From FASTA + ]]></help> + <expand macro="citations" /> +</tool>