Mercurial > repos > iuc > megan_daa_meganizer

annotate daa_meganizer.xml @ 1:f1b6527ba952 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
author iuc
date Tue, 07 Dec 2021 10:17:41 +0000
parents ca7c839a75ab
children bb2a8bd85c85
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
1 <tool id="megan_daa_meganizer" name="MEGAN: meganize a DIAMOND file" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
2 <description>for use with MEGAN</description>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
3 <macros>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
5 </macros>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
6 <expand macro="bio_tools"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
9 ## daa-meganizer "meganizes" the input, altering
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
10 ## the file itself instead of producing a separate
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
11 ## output. We'll make a copy of the input to handle
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
12 ## this issue. The input must also have a .daa file
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
13 ## extension.
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
14 #set input_identifier = 'input.' + $in.ext
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
15 cp '${in}' '${input_identifier}' &&
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
16
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
17 daa-meganizer
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
18 --in '${input_identifier}'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
19 #if $advanced_options.metaDataFile:
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
20 --metaDataFile '$advanced_options.metaDataFile'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
21 #end if
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
22 $advanced_options.longReads
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
23 $advanced_options.classify
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
24 --minScore $advanced_options.minScore
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
25 --maxExpected $advanced_options.maxExpected
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
26 --minPercentIdentity $advanced_options.minPercentIdentity
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
27 --topPercent $advanced_options.topPercent
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
28 --minSupportPercent $advanced_options.minSupportPercent
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
29 --minSupport $advanced_options.minSupport
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
30 --minPercentReadCover $advanced_options.minPercentReadCover
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
31 --minPercentReferenceCover $advanced_options.minPercentReferenceCover
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
32 --minReadLength $advanced_options.minReadLength
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
33 --lcaAlgorithm '$advanced_options.lcaAlgorithm'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
34 --lcaCoveragePercent $advanced_options.lcaCoveragePercent
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
35 --readAssignmentMode '$advanced_options.readAssignmentMode'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
36 #if $advanced_options.conFile:
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
37 --conFile '$advanced_options.conFile'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
38 #end if
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
39 #if $advanced_options.mapDB:
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
40 --mapDB '$advanced_options.mapDB'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
41 #end if
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
42 #if str($advanced_options.only) != '':
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
43 --only '$advanced_options.only'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
44 #end if
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
45 --threads \${GALAXY_SLOTS:-8}
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
46 --tempStoreDir '.'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
47 && mv '$input_identifier' '$output'
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
48 ]]></command>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
49 <inputs>
1
f1b6527ba952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
iuc
parents: 0
diff changeset
50 <expand macro="input_daa_param"/>
0
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
51 <section name="advanced_options" title="Advanced options" expanded="false">
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
52 <param argument="--metaDataFile" type="data" format="tabular" multiple="true" optional="true" label="Files containing metadata to be included in the output files"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
53 <expand macro="long_reads_param"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
54 <expand macro="classify_param"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
55 <expand macro="blast_params"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
56 <expand macro="min_max_params"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
57 <expand macro="lca_params"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
58 <expand macro="read_assignment_mode_param"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
59 <expand macro="con_file_param"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
60 <expand macro="mapdb_param"/>
1
f1b6527ba952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit 374a2824a264468316f04281ed211079015503b5"
iuc
parents: 0
diff changeset
61 <expand macro="only_named_classifications_param"/>
0
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
62 </section>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
63 </inputs>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
64 <outputs>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
65 <data name="output" format="daa"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
66 </outputs>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
67 <tests>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
68 <test>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
69 <param name="in" ftype="daa" value="input.daa"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
70 <output name="output" ftype="daa">
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
71 <assert_contents>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
72 <has_size value="3500"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
73 </assert_contents>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
74 </output>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
75 </test>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
76 </tests>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
77 <help>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
78 **What it does**
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
79
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
80 Meganizes a DIAMOND (i.e., a Direct Access Archive or DAA) file, a proprietary file format developed by PowerISO Computing
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
81 for disk image files. The output is a DIAMOND file consisting of the original input file, but with additional blocks of
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
82 information appended to the end of the file.
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
83
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
84 </help>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
85 <expand macro="citations"/>
ca7c839a75ab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan commit c5facb54a0de925b30cb86f05989e9254d22b89d"
iuc
parents:
diff changeset
86 </tool>