Mercurial > repos > iuc > megan_daa2rma

comparison daa2rma.xml @ 0:e13ac00e6a4d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
author iuc
date Tue, 07 Dec 2021 10:16:58 +0000
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children 10360f9989ee
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-1:000000000000 0:e13ac00e6a4d
1 <tool id="megan_daa2rma" name="MEGAN: Generate a MEGAN rma6 file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>from a DIAMOND daa file</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 #set input_identifier = 'input.' + $in.ext
10 ln -s '${in}' '${input_identifier}' &&
11
12 daa2rma
13 --in '${input_identifier}'
14 #if $advanced_options.metaDataFile:
15 --metaDataFile '$advanced_options.metaDataFile'
16 #end if
17 #if str($advanced_options.paired_reads_cond.paired_reads) == 'yes':
18 --paired
19 $advanced_options.paired_reads_cond.pairedSuffixLength
20 #end if
21 $advanced_options.longReads
22 --maxMatchesPerRead $advanced_options.maxMatchesPerRead
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 --out '$output'
46 --threads \${GALAXY_SLOTS:-8}
47 --tempStoreDir '.'
48 ]]></command>
49 <inputs>
50 <expand macro="input_daa_param"/>
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 <conditional name="paired_reads_cond">
54 <param name="paired_reads" type="select" label="DAA file was created using paired reads?">
55 <option value="no" selected="true">no</option>
56 <option value="yes">Yes</option>
57 </param>
58 <when value="no"/>
59 <when value="yes">
60 <param argument="--pairedSuffixLength" type="integer" value="0" label="Length of name suffix used to distinguish read names" help="Use 0 if read and mate have the same name"/>
61 </when>
62 </conditional>
63 <expand macro="long_reads_param"/>
64 <expand macro="max_matches_per_read_param"/>
65 <expand macro="classify_param"/>
66 <expand macro="blast_params"/>
67 <expand macro="min_max_params"/>
68 <expand macro="lca_params"/>
69 <expand macro="read_assignment_mode_param"/>
70 <expand macro="con_file_param"/>
71 <expand macro="mapdb_param"/>
72 <expand macro="only_named_classifications_param"/>
73 </section>
74 </inputs>
75 <outputs>
76 <data name="output" format="rma6"/>
77 </outputs>
78 <tests>
79 <test>
80 <param name="in" ftype="daa" value="input.daa"/>
81 <output name="output" ftype="rma6">
82 <assert_contents>
83 <has_size value="1487"/>
84 </assert_contents>
85 </output>
86 </test>
87 <test>
88 <param name="in" ftype="daa" value="input.daa"/>
89 <param name="longReads" value="true"/>
90 <param name="minScore" value="25.0"/>
91 <param name="maxExpected" value="0.05"/>
92 <param name="lcaAlgorithm" value="weighted"/>
93 <output name="output" ftype="rma6">
94 <assert_contents>
95 <has_size value="1445"/>
96 </assert_contents>
97 </output>
98 </test>
99 </tests>
100 <help>
101 **What it does**
102
103 Computes a MEGAN RMA (RealMedia Audio) file from a DIOMAND DAA file, a proprietary file format developed by PowerISO Computing
104 for disk image files. MEGAN uses an update of the original RMA file format known as RMA6.
105 </help>
106 <expand macro="citations"/>
107 </tool>