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comparison pslCheck.xml @ 0:ac2c7352c31c draft

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planemo upload commit eec1dc1190352126ba498e7b1bf983edc944d166-dirty
author yating-l
date Wed, 08 Feb 2017 17:42:52 -0500
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1 <?xml version="1.0"?>
2 <tool id="ucsc_pslcheck" name="UCSC pslCheck" version="1.0">
3 <description>validate PSL files</description>
4 <requirements>
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement>
6 </requirements>
7 <stdio>
8 <exit_code range="1:" level="warning" description="invalid entries" />
9 </stdio>
10 <command><![CDATA[
11 faSize -detailed -tab '${query}' > query_sizes
12 && faSize -detailed -tab '${database}' > database_sizes
13 && pslCheck
14 -targetSizes=database_sizes
15 -querySizes=query_sizes
16 -pass='${pass_psl}'
17 '${input_psl}'
18 ]]></command>
19 <inputs>
20 <param type="data" name="database" format="fasta" />
21 <param type="data" name="query" format="fasta" />
22 <param type="data" name="input_psl" format="psl" />
23 </inputs>
24 <outputs>
25 <data format="psl" name="pass_psl" label="${tool.name} on ${on_string}: valid"></data>
26 </outputs>
27 <tests>
28 <test>
29 <param name="database" value="amaVit1_Gallus/amaVit1.fa" />
30 <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" />
31 <param name="input_psl" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered.psl" />
32 <output name="pass_psl" value="amaVit1_Gallus/amaVit1_Gallus_gallus_filtered_valid.psl" />
33 </test>
34 <test>
35 <param name="database" value="dbia3/dbia3.fa" />
36 <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" />
37 <param name="input_psl" value="dbia3/dbia3_dmel_filtered.psl" />
38 <output name="pass_psl" value="dbia3/dbia3_dmel_filtered_valid.psl" />
39 </test>
40
41 </tests>
42 <help>
43 <![CDATA[
44 pslCheck - validate PSL files
45 ==============================
46
47 usage:
48
49 $ pslCheck fileTbl(s)
50
51 options:
52
53 -pass=pslFile - write PSLs without errors to this file
54
55 -targetSizes=sizesFile - tab file with columns of target and size.
56
57 If specified, psl is check to have a valid target and target
58 coordinates.
59
60 -querySizes=sizesFile - file with query sizes.
61
62 Source code (v340):
63 ++++++++++++++++++++
64
65 userApps.v340.src.tgz: http://hgdownload.cse.ucsc.edu/admin/exe/
66
67 ]]></help>
68 <citations>
69 <citation type="bibtex">@article{kent2002blat,
70 title={BLAT—the BLAST-like alignment tool},
71 author={Kent, W James},
72 journal={Genome research},
73 volume={12},
74 number={4},
75 pages={656--664},
76 year={2002},
77 publisher={Cold Spring Harbor Lab}
78 }</citation>
79 </citations>
80 </tool>
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