Mercurial > repos > galaxyp > sixgill
comparison sixgill_makefasta.xml @ 0:cf8eee8343fb draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty
author | galaxyp |
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date | Thu, 13 Oct 2016 08:38:04 -0400 |
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1 <tool id="sixgill_makefasta" name="sixgill makefasta" version="@VERSION@.0"> | |
2 <description>from a metapeptide database</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <expand macro="stdio" /> | |
8 <version_command>sixgill_makefasta --version</version_command> | |
9 <command><![CDATA[ | |
10 sixgill_makefasta | |
11 --out=metapeptides_fa_output.fa | |
12 --type="$fa_type.fasta_type" | |
13 #if $fa_type.fasta_type == 'peptide': | |
14 --missedcleavages=$fa_type.missedcleavages | |
15 --minpeptidelength=$fa_type.minpeptidelength | |
16 #end if | |
17 "$metapeptide_db" | |
18 ]]></command> | |
19 <inputs> | |
20 <param name="metapeptide_db" type="data" format="tabular" label="metapeptide database" | |
21 help="Can be generated with sixgill_build"/> | |
22 <conditional name="fa_type"> | |
23 <param name="fasta_type" type="select" label="fasta type"> | |
24 <help> peptide with specified missed cleavages requires holding | |
25 all peptides in the database in memory, as each is only written once | |
26 </help> | |
27 <option value="aa" selected="true">aa - amino acid</option> | |
28 <option value="peptide">peptide - with specified missed cleavages</option> | |
29 </param> | |
30 <when value="aa"/> | |
31 <when value="peptide"> | |
32 <param name="missedcleavages" type="integer" value="0" min="0" max="6" label="missedcleavages"/> | |
33 <param name="minpeptidelength" type="integer" value="7" min="1" label="minpeptidelength"/> | |
34 </when> | |
35 </conditional> | |
36 | |
37 </inputs> | |
38 <outputs> | |
39 <data name="output_fa" format="fasta" label="${tool.name} on ${on_string}: metapeptide.fa" from_work_dir="metapeptides_fa_output.fa"/> | |
40 </outputs> | |
41 <tests> | |
42 <test> | |
43 <param name="metapeptide_db" ftype="tabular" value="testdb_metagene.metapeptides.tsv"/> | |
44 <param name="fasta_type" value="aa"/> | |
45 <output name="output_fa"> | |
46 <assert_contents> | |
47 <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" /> | |
48 </assert_contents> | |
49 </output> | |
50 </test> | |
51 </tests> | |
52 <help><![CDATA[ | |
53 usage: sixgill_makefasta [-h] --out OUT --type {aa,peptide} | |
54 [--missedcleavages MISSEDCLEAVAGES] | |
55 [--minpeptidelength MINPEPTIDELENGTH] [--debug] | |
56 metapeptidedbfile | |
57 | |
58 Build a fasta database from a metapeptide database. Either nucleotide or amino | |
59 acid. | |
60 | |
61 positional arguments: | |
62 metapeptidedbfile input metapeptide database file | |
63 | |
64 optional arguments: | |
65 -h, --help show this help message and exit | |
66 --out OUT output file | |
67 --type {aa,peptide} database type | |
68 --missedcleavages MISSEDCLEAVAGES | |
69 missed cleavages (for type peptide only) | |
70 --minpeptidelength MINPEPTIDELENGTH | |
71 minimum peptide length (for type peptide only) | |
72 --debug Enable debug logging | |
73 | |
74 ]]></help> | |
75 <expand macro="citations" /> | |
76 </tool> |