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comparison pi_dbspec_align.xml @ 2:77ddaee887a8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
author galaxyp
date Fri, 01 Sep 2017 03:14:54 -0400
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children 78afc81ab244
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1:8a30d6e5b97d 2:77ddaee887a8
1 <tool id="pi_dbspec_align" name="Align DB fractions" version="0.3">
2 <description>to resemble spectra fraction scheme</description>
3 <requirements>
4 <requirement type="package" version="3.6">python</requirement>
5 <requirement type="package" version="1.62">biopython</requirement>
6 </requirements>
7 <command detect_errors="exit_code">
8 <![CDATA[
9 mkdir aligned_out &&
10 python '$__tool_directory__/align_dbspec.py'
11 --specnames $specnames
12 --dbfiles
13 #for $key in $databases.keys()
14 '$databases[$key]'
15 #end for
16 --frspec '$frspec'
17 --firstfr $firstfr
18
19 ]]>
20 </command>
21
22 <inputs>
23 <param name="specnames" type="data" format="text,tabular" label="Spectra files" />
24 <param name="databases" type="data_collection" collection_type="list" format="fasta" label="Fractionated databases" />
25 <param name="frspec" type="text" label="Regex to find fraction numbers in spectra file names" help="If spectra file is called myspectra_fr01b.mzML, use .*fr([0-9]+).*" >
26 <sanitizer>
27 <valid initial="string.printable">
28 <remove value="&apos;"/>
29 </valid>
30 </sanitizer>
31 </param>
32 <param name="firstfr" type="integer" value="1" label="First fraction number in series" />
33 </inputs>
34
35 <outputs>
36 <collection name="aligned_db" type="list" label="spectra-fraction-aligned DB">
37 <discover_datasets pattern="__designation__" ext="fasta" directory="aligned_out" />
38 </collection>
39 </outputs>
40 <tests>
41 <test>
42 <param name="specnames" value="specnames.txt" />
43 <param name="databases">
44 <collection type="list">
45 <element name="fr1" value="target_splitdb_fr1.fasta" />
46 <element name="fr2" value="target_splitdb_fr2.fasta" />
47 <element name="fr3" value="target_splitdb_fr3.fasta" />
48 <element name="fr4" value="decoy_splitdb_fr1.fasta" />
49 <element name="fr5" value="decoy_splitdb_fr2.fasta" />
50 <element name="fr6" value="decoy_splitdb_fr3.fasta" />
51 <element name="fr7" value="decoy_splitdb_fr1.fasta" />
52 <element name="fr8" value="decoy_splitdb_fr2.fasta" />
53 <element name="fr9" value="decoy_splitdb_fr3.fasta" />
54 </collection>
55 </param>
56 <param name="frspec" value=".*c_f([0-9]+).*" />
57 <param name="firstfr" value="1" />
58 <output_collection name="aligned_db" type="list">
59 <element name="spec_f01.mzML" value="target_splitdb_fr1.fasta" />
60 <element name="spec_f02.mzML" value="target_splitdb_fr2.fasta" />
61 <element name="spec_f03.mzML" value="target_splitdb_fr3.fasta" />
62 <element name="spec_f03b.mzML" value="target_splitdb_fr3.fasta" />
63 <element name="spec_f09.mzML" value="merged_twice_decoy_fr1-3.fasta" compare="sim_size" />
64 <element name="spec_f09b.mzML" value="merged_twice_decoy_fr1-3.fasta" compare="sim_size" />
65 </output_collection>
66 </test>
67 </tests>
68
69 <help>
70 Filters, pools and doubles fractionated databases with a set of identically fractionated spectra files which have been
71 subjected to pooling and contain reruns.
72 You may have fraction 1-10 in databases but spectra file fractions 4-7 have been pooled before loading to the MS,
73 and spectra fraction 2 and 8 have been reran creating fractions 2 and 2a, and 8, 8a and 8b.
74 This tool pools FASTA databases and duplicates them where needed to line up the databases to your spectra collections.
75 </help>
76
77 </tool>