Mercurial > repos > iuc > mapseq

annotate mapseq.xml @ 0:16f561c480bb draft default tip

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/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
author iuc
date Mon, 14 Oct 2024 12:27:57 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
1 <tool id="mapseq" name="MAPseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
2 <description>sequence read classification designed to assign taxonomy and OTU classifications</description>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
3 <macros>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
4 <token name="@TOOL_VERSION@">2.1.1b</token>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
6 </macros>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
7 <xrefs>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
8 <xref type="bio.tools">mapseq</xref>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
9 </xrefs>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
10 <requirements>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
11 <requirement type="package" version="5.26">perl</requirement>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
12 <requirement type="package" version="@TOOL_VERSION@">mapseq</requirement>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
13 </requirements>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
14 <command detect_errors="exit_code"><![CDATA[
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
15
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
16 #if $ref_db.db_source == "cached" and $ref_db.mapseq2biom.mapseq2biom == "no":
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
17 ln -s '${ref_db.db_cached.fields.path}'/*.fasta db.fasta &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
18 ln -s '${ref_db.db_cached.fields.path}'/*.txt taxonomy.txt &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
19 ln -s '${ref_db.db_cached.fields.path}'/*.mscluster db.fasta.mscluster &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
20 #end if
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
21
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
22 #if $ref_db.db_source == "cached" and $ref_db.mapseq2biom.mapseq2biom == "yes":
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
23 ln -s '${ref_db.db_cached.fields.path}'/*.fasta db.fasta &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
24 ln -s '${ref_db.db_cached.fields.path}'/*.txt taxonomy.txt &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
25 ln -s '${ref_db.db_cached.fields.path}'/*.mscluster db.fasta.mscluster &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
26 ln -s '${ref_db.db_cached.fields.path}'/*.otu db.otu &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
27 #end if
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
28
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
29 #if $ref_db.db_source == "history" and $ref_db.mapseq2biom.mapseq2biom == "no":
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
30 ln -s '${ref_db.database}' db.fasta &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
31 ln -s '${ref_db.taxonomy}' taxonomy.txt &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
32 ln -s '${ref_db.mscluster}' db.fasta.mscluster &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
33 #end if
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
34
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
35 #if $ref_db.db_source == "history" and $ref_db.mapseq2biom.mapseq2biom == "yes":
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
36 ln -s '${ref_db.database}' db.fasta &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
37 ln -s '${ref_db.taxonomy}' taxonomy.txt &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
38 ln -s '${ref_db.mscluster}' db.fasta.mscluster &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
39 ln -s '${ref_db.mapseq2biom.otu_table}' db.otu &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
40 #end if
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
41 mapseq
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
42 -nthreads \${GALAXY_SLOTS:-8}
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
43 #if str($seed) != ""
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
44 -seed '$seed'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
45 #end if
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
46 -tophits '$tophits'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
47 -topotus '$topotus'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
48 -minscore '$minscore'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
49 -minid1 '$minid1'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
50 -minid2 '$minid2'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
51 -otulim '$otulim'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
52 -outfmt '$outfmt'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
53 '$sequences' db.fasta taxonomy.txt > '$classifications'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
54
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
55 #if $ref_db.mapseq2biom.mapseq2biom == "yes":
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
56 &&
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
57 perl '$__tool_directory__/mapseq2biom.pl' --otuTable db.otu --query '$classifications' --outfile '$otu_tsv' --taxid --notaxidfile '$otu_tsv_notaxid'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
58 #if $ref_db.mapseq2biom.krona_input == 'yes':
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
59 --krona '$krona_format'
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
60 #end if
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
61 #end if
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
62
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
63 ]]></command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
64
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
65 <inputs>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
66 <param type="data" name="sequences" format="fasta" label="Input sequences" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
67 <conditional name="ref_db">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
68 <param name="db_source" type="select" label="Use cached database or database from history" help="">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
69 <option value="cached">Cached database</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
70 <option value="history">From history</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
71 </param>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
72 <when value="cached">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
73 <param name="db_cached" type="select" label="Using built-in mapseq DB" help="">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
74 <options from_data_table="mapseq_db">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
75 <column name="value" index="0" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
76 <column name="name" index="1" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
77 <column name="version" index="2" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
78 <column name="path" index="3" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
79 <filter type="sort_by" column="1"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
80 </options>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
81 <validator type="no_options" message="A built-in mapseq DB is not available. Please ask the Galaxy admins to install one on the server." />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
82 </param>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
83 <conditional name="mapseq2biom">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
84 <param type="select" name="mapseq2biom" label="Create OTU table" help="Creates a tab-separated OTU table (including taxonomy classification) that can be used to create BIOM files">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
85 <option value="yes">Yes</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
86 <option value="no">No</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
87 </param>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
88 <when value="yes">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
89 <param type="boolean" name="krona_input" truevalue="yes" falsevalue="no" label="Create taxon table for Krona" help="Generates a reads per taxon file suitable for the use with Krona" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
90 </when>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
91 <when value="no" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
92 </conditional>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
93 </when>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
94 <when value="history">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
95 <param type="data" name="database" label="Database file (FASTA format)" format="fasta" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
96 <param type="data" name="taxonomy" label="Taxonomy file" format="tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
97 <param type="data" name="mscluster" label="Database cluster" format="txt" optional="true" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
98 <conditional name="mapseq2biom">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
99 <param type="select" name="mapseq2biom" label="Create out of the MAPseq output a tab-separated output file?">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
100 <option value="yes">Yes</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
101 <option value="no">No</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
102 </param>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
103 <when value="yes">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
104 <param type="data" name="otu_table" format="txt" label="OTU table" help="The OTU table produced for the taxonomies found in the reference databases that was used with MAPseq" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
105 <param type="boolean" name="krona_input" truevalue="yes" falsevalue="no" help="Generates an output file suitable for the use with Krona" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
106 </when>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
107 <when value="no" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
108 </conditional>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
109 </when>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
110 </conditional>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
111
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
112 <param argument="-seed" type="integer" label="Fix random seed" help="Sets a fixed integer seed value for random number generation, ensuring reproducible results" optional="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
113
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
114 <param argument="-tophits" type="integer" label="Top hits" help="Number of reference sequences to include in alignment phase"
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
115 value="20" min="1" max="200" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
116
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
117 <param argument="-topotus" type="integer" label="Top OTUs" help="Number of internal reference otus to include in alignment phase"
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
118 value="10" min="1" max="200" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
119
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
120 <param argument="-minscore" type="integer" label="Minimum score"
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
121 help="Minimum score cutoff to consider for a classification, should be reduced when searching very small sequences, i.e.: primer search"
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
122 value="30" min="1" max="50" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
123
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
124 <param argument="-minid1" type="integer" label="Minimum number of shared kmers" help="Minimum number of shared kmers to consider hit in second phase kmer search"
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
125 value="1" min="1" max="10" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
126
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
127 <param argument="-minid2" type="integer" label="Number of ref. sequences" help="Number of reference sequences to include in alignment phase"
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
128 value="1" min="1" max="10" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
129
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
130 <param argument="-otulim" type="integer" label="OTU limit" help="Minimum number of shared kmers to consider hit in alignment phase"
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
131 value="50" min="1" max="60" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
132
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
133 <param argument="-outfmt" type="select" label="Output format" help="The `confidences` format outputs confidence values for each of the taxonomic levels. ">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
134 <option value="simple">simple</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
135 <option value="confidences">confidences</option>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
136 </param>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
137 </inputs>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
138
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
139 <outputs>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
140 <data format="tabular" name="classifications" label="Classification results"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
141 <data name="otu_tsv" format="tabular" label="tab-output including taxIDs">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
142 <filter>(ref_db['mapseq2biom']['mapseq2biom'] == "yes")</filter>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
143 </data>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
144 <data name="otu_tsv_notaxid" format="tabular" label="tab-output without taxIDs" >
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
145 <filter>(ref_db['mapseq2biom']['mapseq2biom'] == "yes")</filter>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
146 </data>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
147 <data name="krona_format" format="tabular" label="Krona input" >
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
148 <filter>(ref_db['mapseq2biom']['mapseq2biom'] == "yes" and ref_db['mapseq2biom']['krona_input'])</filter>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
149 </data>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
150 </outputs>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
151
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
152 <tests>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
153 <test expect_num_outputs="1">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
154 <param name="db_source" value="history" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
155 <param name="sequences" value="sequences.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
156 <param name="database" value="mapseq_db/LSU_trimmed.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
157 <param name="taxonomy" value="mapseq_db/slv_lsu_filtered2_trimmed.txt"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
158 <param name="mscluster" value="mapseq_db/LSU_trimmed.fasta.mscluster"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
159 <param name="mapseq2biom" value="no"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
160 <output name="classifications" file="sequences.mapseq" sort="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
161 <assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
162 <has_text text="-seed" negate="true" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
163 </assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
164 </test>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
165 <test expect_num_outputs="1">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
166 <param name="db_source" value="history" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
167 <param name="sequences" value="sequences.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
168 <param name="database" value="mapseq_db/LSU_trimmed.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
169 <param name="taxonomy" value="mapseq_db/slv_lsu_filtered2_trimmed.txt"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
170 <param name="mapseq2biom" value="no"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
171 <output name="classifications" file="sequences.mapseq" sort="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
172 <assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
173 <has_text text="-seed" negate="true" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
174 </assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
175 </test>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
176 <test expect_num_outputs="3">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
177 <param name="db_source" value="history" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
178 <param name="sequences" value="sequences.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
179 <param name="database" value="mapseq_db/LSU_trimmed.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
180 <param name="taxonomy" value="mapseq_db/slv_lsu_filtered2_trimmed.txt"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
181 <param name="mscluster" value="mapseq_db/LSU_trimmed.fasta.mscluster"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
182 <param name="mapseq2biom" value="yes"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
183 <param name="krona_input" value="no"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
184 <param name="otu_table" value="mapseq_db/test.otu" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
185 <param name="seed" value="12" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
186 <output name="classifications" file="sequences.mapseq" sort="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
187 <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
188 <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
189 <assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
190 <has_text text="-seed '12'" n="1" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
191 </assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
192 </test>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
193 <test expect_num_outputs="4">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
194 <param name="db_source" value="history" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
195 <param name="sequences" value="sequences.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
196 <param name="database" value="mapseq_db/LSU_trimmed.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
197 <param name="taxonomy" value="mapseq_db/slv_lsu_filtered2_trimmed.txt"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
198 <param name="mscluster" value="mapseq_db/LSU_trimmed.fasta.mscluster"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
199 <param name="mapseq2biom" value="yes"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
200 <param name="krona_input" value="yes"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
201 <param name="otu_table" value="mapseq_db/test.otu" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
202 <output name="classifications" file="sequences.mapseq" sort="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
203 <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
204 <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
205 <output name="krona_format" file="mapseq2biom/krona_input.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
206 <assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
207 <has_text text="-seed" negate="true" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
208 </assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
209 </test>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
210 <test expect_num_outputs="1">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
211 <param name="db_source" value="cached" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
212 <param name="db_cached" value="test_mapseq_db" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
213 <param name="sequences" value="sequences.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
214 <param name="mapseq2biom" value="no"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
215 <output name="classifications" file="sequences.mapseq" sort="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
216 <assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
217 <has_text text="-seed" negate="true" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
218 </assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
219 </test>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
220 <test expect_num_outputs="3">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
221 <param name="db_source" value="cached" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
222 <param name="db_cached" value="test_mapseq_db" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
223 <param name="sequences" value="sequences.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
224 <param name="mapseq2biom" value="yes"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
225 <param name="krona_input" value="no"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
226 <output name="classifications" file="sequences.mapseq" sort="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
227 <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
228 <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
229 <assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
230 <has_text text="-seed" negate="true" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
231 </assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
232 </test>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
233 <test expect_num_outputs="4">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
234 <param name="db_source" value="cached" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
235 <param name="db_cached" value="test_mapseq_db" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
236 <param name="sequences" value="sequences.fasta"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
237 <param name="mapseq2biom" value="yes"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
238 <param name="krona_input" value="yes"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
239 <param name="seed" value="12" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
240 <output name="classifications" file="sequences.mapseq" sort="true"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
241 <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
242 <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
243 <output name="krona_format" file="mapseq2biom/krona_input.tabular" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
244 <assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
245 <has_text text="-seed '12'" n="1" />
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
246 </assert_command>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
247 </test>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
248 </tests>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
249
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
250 <help><![CDATA[
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
251 MAPseq
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
252 ======
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
253 MAPseq is a set of fast and accurate sequence read classification tools
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
254 designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
255 This is done by using a reference set of full-length ribosomal RNA sequences
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
256 for which known taxonomies are known, and for which a set of high quality
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
257 OTU clusters has been previously generated. For each read, the best guess
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
258 and correspoding confidence in the assignment is shown at each taxonomic and OTU level.
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
259
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
260 Mapseq2biom
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
261 ===========
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
262 This downstream script summaries the mapseq output as an OTU table
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
263 (including taxon information) as reads per OTU. This requires as input
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
264 an OTU to taxon mapping, for the taxonomy used to run the mapseq tool.
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
265
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
266
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
267 Example
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
268 -------
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
269
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
270 Mapseq output:
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
271
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
272 ::
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
273
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
274 # mapseq v1.2.3 (Oct 2 2018)
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
275 #query dbhit bitscore identity matches mismatches gaps query_start query_end dbhit_start dbhit_end strand ITS2
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
276 test.1 355527192 204 0.9863636493682861 217 1 2 0 218 0 220 - sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Didymellaceae;g__Ectophoma;s__Ectophoma_multirostrata
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
277 test.2 555948006 248 0.8478803038597107 340 42 19 200 582 192 593 - sk__Eukaryota;k__Fungi
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
278 test.4 406352048 217 0.9127272963523865 251 22 2 106 381 169 442 - sk__Eukaryota;k__Fungi;p__
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
279
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
280 OTU to taxon mapping:
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
281
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
282 ::
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
283
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
284 1 sk__Eukaryota;k__Fungi
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
285 2 sk__Eukaryota;k__Fungi;p__;c__;o__;f__;g__;s__uncultured_fungus
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
286 3 sk__Eukaryota;k__Fungi;p__Ascomycota
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
287 4 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
288 5 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Astrosphaeriellaceae;g__Pithomyces
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
289 6 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Coniothyriaceae;g__Coniothyrium
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
290 7 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Didymellaceae
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
291 8 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Didymellaceae;g__Ectophoma
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
292 9 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Didymellaceae;g__Ectophoma;s__Ectophoma_multirostrata
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
293 10 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Didymosphaeriaceae;g__Paraconiothyrium;s__Paraconiothyrium_cyclothyrioides
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
294
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
295 OTU output:
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
296
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
297 ::
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
298
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
299 # Constructed from biom file
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
300 # OTU ID label taxonomy
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
301 1 2.0 sk__Eukaryota;k__Fungi
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
302 9 1.0 sk__Eukaryota;k__Fungi;p__Ascomycota;c__Dothideomycetes;o__Pleosporales;f__Didymellaceae;g__Ectophoma;s__Ectophoma_multirostrata
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
303
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
304 Taxon output for Krona:
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
305
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
306 ::
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
307
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
308 2 sk__Eukaryota k__Fungi
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
309 1 sk__Eukaryota k__Fungi p__Ascomycota c__Dothideomycetes o__Pleosporales f__Didymellaceae g__Ectophoma s__Ectophoma_multirostrata
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
310
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
311 Source
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
312 ------
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
313 * `GitHub <https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/mapseq2biom/mapseq2biom.pl>`_
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
314
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
315 License
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
316 -------
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
317 * `Apache-2.0 license <https://raw.githubusercontent.com/EBI-Metagenomics/pipeline-v5/master/LICENSE>`_
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
318 ]]></help>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
319 <creator>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
320 <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
321 <person givenName="Paul" familyName="Zierep" url="https://github.com/paulzierep"/>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
322 </creator>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
323 <citations>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
324 <citation type="doi">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
325 10.1093/bioinformatics/btx517
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
326 </citation>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
327 <citation type="doi">
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
328 10.1093/nar/gkac1080
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
329 </citation>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
330 </citations>
16f561c480bb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
iuc
parents:
diff changeset
331 </tool>