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comparison smart_domains.xml @ 0:a3b26189fee3 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains commit 266d7c45a443e893f15eab4b1485ca7c1c406a14
author earlhaminst
date Thu, 15 Jun 2017 07:52:09 -0400
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-1:000000000000 0:a3b26189fee3
1 <tool id="smart_domains" name="SMART domains" version="0.1.0">
2 <description>Search domains in protein sequences using SMART</description>
3 <requirements>
4 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
5 <requirement type="package" version="2.90">perl-json</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 perl '$__tool_directory__/smart-domain.pl'
9 --inputFile='$inputFile'
10 $Pfam
11 $SignalP
12 $Repeats
13 $DISEMBL
14 $Schnipsel
15 $outputFormat
16 ]]></command>
17 <inputs>
18 <param name="inputFile" type="data" format="fasta" label="Protein sequences" help="In FASTA format" />
19 <param name="Pfam" type="boolean" truevalue="--includePfam" falsevalue="" label="Include Pfam domains" argument="--includePfam" />
20 <param name="SignalP" type="boolean" truevalue="--includeSignalP" falsevalue="" label="Include signal peptide predictions" argument="--includeSignalP" />
21 <param name="Repeats" type="boolean" truevalue="--includeRepeats" falsevalue="" label="Include internal repeat predictions" argument="--includeRepeats" />
22 <param name="DISEMBL" type="boolean" truevalue="--includeDISEMBL" falsevalue="" label="Include predictions of internal protein disorder" argument="--includeDISEMBL" />
23 <param name="Schnipsel" type="boolean" truevalue="--includeSchnipsel" falsevalue="" label="Include predictions of outlier homologues and homologues of known structures" argument="--includeSchnipsel" />
24 <param name="outputFormat" type="select" label="Output format">
25 <option value="--outputFormat=txt" selected="true">Text</option>
26 <option value="--outputFormat=tabular">Tabular</option>
27 <option value="--outputFormat=json">JSON</option>
28 </param>
29 </inputs>
30 <outputs>
31 <collection name="output_lists" type="list" label="${tool.name} on ${on_string}">
32 <discover_datasets pattern="(?P&lt;name&gt;.+)_SMART_results\.(?P&lt;ext&gt;.+)" directory="SMART_results" />
33 </collection>
34 </outputs>
35 <tests>
36 <test>
37 <param name="inputFile" ftype="fasta" value="seq.fa" />
38 <param name="Pfam" value="true" />
39 <param name="SignalP" value="false" />
40 <param name="Repeats" value="false" />
41 <param name="DISEMBL" value="false" />
42 <param name="Schnipsel" value="false" />
43 <param name="outputFormat" value="--outputFormat=txt" />
44 <output_collection name="output_lists" type="list" count="12">
45 <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.txt" ftype="txt" />
46 <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.txt" ftype="txt" />
47 <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.txt" ftype="txt" />
48 <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.txt" ftype="txt" />
49 <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.txt" ftype="txt" />
50 <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.txt" ftype="txt" />
51 <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.txt" ftype="txt" />
52 <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.txt" ftype="txt" />
53 <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.txt" ftype="txt" />
54 <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.txt" ftype="txt" />
55 <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.txt" ftype="txt" />
56 <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.txt" ftype="txt" />
57 </output_collection>
58 </test>
59 <test>
60 <param name="inputFile" ftype="fasta" value="seq.fa" />
61 <param name="Pfam" value="true" />
62 <param name="SignalP" value="false" />
63 <param name="Repeats" value="false" />
64 <param name="DISEMBL" value="false" />
65 <param name="Schnipsel" value="false" />
66 <param name="outputFormat" value="--outputFormat=json" />
67 <output_collection name="output_lists" type="list" count="12">
68 <element name="ENSCAFP00000021307" file="ENSCAFP00000021307_SMART_results.json" ftype="json" compare="sim_size" />
69 <element name="ENSCAFP00000021330" file="ENSCAFP00000021330_SMART_results.json" ftype="json" compare="sim_size" />
70 <element name="ENSMUSP00000026013" file="ENSMUSP00000026013_SMART_results.json" ftype="json" compare="sim_size" />
71 <element name="ENSMUSP00000040550" file="ENSMUSP00000040550_SMART_results.json" ftype="json" compare="sim_size" />
72 <element name="ENSP00000340684" file="ENSP00000340684_SMART_results.json" ftype="json" compare="sim_size" />
73 <element name="ENSP00000367309" file="ENSP00000367309_SMART_results.json" ftype="json" compare="sim_size" />
74 <element name="ENSPTRP00000037440" file="ENSPTRP00000037440_SMART_results.json" ftype="json" compare="sim_size" />
75 <element name="ENSPTRP00000037441" file="ENSPTRP00000037441_SMART_results.json" ftype="json" compare="sim_size" />
76 <element name="ENSRNOP00000043466" file="ENSRNOP00000043466_SMART_results.json" ftype="json" compare="sim_size" />
77 <element name="ENSRNOP00000063784" file="ENSRNOP00000063784_SMART_results.json" ftype="json" compare="sim_size" />
78 <element name="ENSSSCP00000013044" file="ENSSSCP00000013044_SMART_results.json" ftype="json" compare="sim_size" />
79 <element name="ENSSSCP00000028353" file="ENSSSCP00000028353_SMART_results.json" ftype="json" compare="sim_size" />
80 </output_collection>
81 </test>
82 </tests>
83 <help><![CDATA[
84 A simple tool to search domains in multiple protein sequences contained in a FASTA file using the `SMART`_ web service.
85
86 Written by Ivica Letunic <ivica@letunic.com>
87
88 Modified by Anil Thanki <Anil.Thanki@earlham.ac.uk> to parse output in JSON and tabular format to adapt in Galaxy
89
90 .. _SMART: http://smart.embl.de/
91 ]]></help>
92 <citations>
93 <citation type="doi">10.1073/pnas.95.11.5857</citation>
94 <citation type="doi">10.1093/nar/gku949</citation>
95 </citations>
96 </tool>