Mercurial > repos > jjohnson > encyclopedia_fasta_to_prosit_csv

comparison encyclopedia_fasta_to_prosit_csv.xml @ 0:d0202c597434 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia commit 8f99967c46243d2ad661287ce6d17c5824dbc533-dirty"
author jjohnson
date Fri, 19 Jun 2020 10:21:58 -0400
parents
children 91343296dbff
comparison
equal deleted inserted replaced
-1:000000000000 0:d0202c597434
1 <tool id="encyclopedia_fasta_to_prosit_csv" name="ConvertFastaToPrositCSV" version="@VERSION@.0" python_template_version="3.5">
2 <description>Create Prosit CSV Input From a Protein FASTA</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 EncyclopeDIA -convert -fastatoprositcsv
9 -i '$i'
10 -minCharge $minCharge
11 -maxCharge $maxCharge
12 -defaultCharge $defaultCharge
13 -maxMissedCleavage $maxMissedCleavage
14 -minMz $minMz
15 -maxMz $maxMz
16 -defaultNCE $defaultNCE
17 #if $enzyme
18 -enzyme '$enzyme'
19 #end if
20 -o '$output'
21 ]]></command>
22 <inputs>
23 <param argument="-i" type="data" format="fasta" label="Protein Fasta database"/>
24 <param argument="-minCharge" type="integer" value="2" min="1" max="6" label="minCharge" help="(default: 2)"/>
25 <param argument="-maxCharge" type="integer" value="3" min="1" max="6" label="maxCharge" help="(default: 3)"/>
26 <param argument="-defaultCharge" type="integer" value="3" min="1" max="4" label="defaultCharge" help="(default: 3)"/>
27 <param argument="-maxMissedCleavage" type="integer" value="1" min="0" max="3" label="maxMissedCleavage" help="(default: 1)"/>
28 <param argument="-minMz" type="float" value="396.4" min="150.0" max="1600.0" label="minMz" help="(default: 396.4)"/>
29 <param argument="-maxMz" type="float" value="1002.7" min="150.0" max="1600.0" label="maxMz" help="(default: 1002.7)"/>
30 <param argument="-defaultNCE" type="integer" value="33" min="25" max="40" label="Normalized Collision Energy" help="(default: 33)"/>
31 <param argument="-enzyme" type="select" optional="true" label="Digestion Enzyme" help="(default: Trypsin)">
32 <option value="Trypsin">Trypsin</option>
33 <option value="Lys-C">Lys-C</option>
34 <option value="Lys-N">Lys-N</option>
35 <option value="Arg-C">Arg-C</option>
36 <option value="Glu-C">Glu-C</option>
37 <option value="CNBr">CNBr</option>
38 <option value="Chymotrypsin">Chymotrypsin</option>
39 <option value="Pepsin A">Pepsin A</option>
40 <option value="No Enzyme">No Enzyme</option>
41 </param>
42 </inputs>
43 <outputs>
44 <data name="output" format="csv" label="${i.name} Prosit_input.csv"/>
45 </outputs>
46 <tests>
47 <test>
48 <param name="i" ftype="fasta" value="YeastProteinFasta5.fasta"/>
49 <output name="output" ftype="csv">
50 <assert_contents>
51 <has_text text="collision_energy"/>
52 <has_text text="EDFFTVFDSLLR"/>
53 </assert_contents>
54 </output>
55 </test>
56 </tests>
57 <help><![CDATA[
58 Create Prosit CSV From FASTA
59 ]]></help>
60 <expand macro="citations" />
61 </tool>