Mercurial > repos > iuc > megan_daa_meganizer

comparison daa_meganizer.xml @ 0:ca7c839a75ab draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
author iuc
date Fri, 03 Dec 2021 23:10:15 +0000
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children f1b6527ba952
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-1:000000000000 0:ca7c839a75ab
1 <tool id="megan_daa_meganizer" name="MEGAN: meganize a DIAMOND file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>for use with MEGAN</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ## daa-meganizer "meganizes" the input, altering
10 ## the file itself instead of producing a separate
11 ## output. We'll make a copy of the input to handle
12 ## this issue. The input must also have a .daa file
13 ## extension.
14 #set input_identifier = 'input.' + $in.ext
15 cp '${in}' '${input_identifier}' &&
16
17 daa-meganizer
18 --in '${input_identifier}'
19 #if $advanced_options.metaDataFile:
20 --metaDataFile '$advanced_options.metaDataFile'
21 #end if
22 $advanced_options.longReads
23 $advanced_options.classify
24 --minScore $advanced_options.minScore
25 --maxExpected $advanced_options.maxExpected
26 --minPercentIdentity $advanced_options.minPercentIdentity
27 --topPercent $advanced_options.topPercent
28 --minSupportPercent $advanced_options.minSupportPercent
29 --minSupport $advanced_options.minSupport
30 --minPercentReadCover $advanced_options.minPercentReadCover
31 --minPercentReferenceCover $advanced_options.minPercentReferenceCover
32 --minReadLength $advanced_options.minReadLength
33 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
34 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
35 --readAssignmentMode '$advanced_options.readAssignmentMode'
36 #if $advanced_options.conFile:
37 --conFile '$advanced_options.conFile'
38 #end if
39 #if $advanced_options.mapDB:
40 --mapDB '$advanced_options.mapDB'
41 #end if
42 #if str($advanced_options.only) != '':
43 --only '$advanced_options.only'
44 #end if
45 --threads \${GALAXY_SLOTS:-8}
46 --tempStoreDir '.'
47 && mv '$input_identifier' '$output'
48 ]]></command>
49 <inputs>
50 <param argument="--in" type="data" format="daa" label="Input DAA file"/>
51 <section name="advanced_options" title="Advanced options" expanded="false">
52 <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
53 <expand macro="long_reads_param"/>
54 <expand macro="classify_param"/>
55 <expand macro="blast_params"/>
56 <expand macro="min_max_params"/>
57 <expand macro="lca_params"/>
58 <expand macro="read_assignment_mode_param"/>
59 <expand macro="con_file_param"/>
60 <expand macro="mapdb_param"/>
61 <param argument="--only" type="text" value="" label="Names of classifications to use" help="Leave blank to use all classifications">
62 <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
63 </param>
64 </section>
65 </inputs>
66 <outputs>
67 <data name="output" format="daa"/>
68 </outputs>
69 <tests>
70 <test>
71 <param name="in" ftype="daa" value="input.daa"/>
72 <output name="output" ftype="daa">
73 <assert_contents>
74 <has_size value="3500"/>
75 </assert_contents>
76 </output>
77 </test>
78 </tests>
79 <help>
80 **What it does**
81
82 Meganizes a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
83 for disk image files. The output is a DIAMOND file consisting of the original input file, but with additional blocks of
84 information appended to the end of the file.
85
86 </help>
87 <expand macro="citations"/>
88 </tool>