Mercurial > repos > iuc > kraken_taxonomy_report

annotate kraken_taxonomy_report.xml @ 5:bfae8da6082c 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/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
author iuc
date Tue, 12 Mar 2024 09:52:55 +0000
parents 27d65c78863c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
1 <tool id="kraken_taxonomy_report" name="Kraken taxonomic report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="16.04">
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
2 <description>view report of classification for multiple samples</description>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
3 <macros>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
4 <token name="@TOOL_VERSION@">0.0.3</token>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
6 </macros>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
7 <xrefs>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
8 <xref type="bio.tools">Kraken-Taxonomy-Report</xref>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
9 </xrefs>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
10 <requirements>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
11 <requirement type="package" version="1.66">biopython</requirement>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
12 </requirements>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
13
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
14 <version_command>python '${__tool_directory__}/kraken_taxonomy_report.py' --version</version_command>
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
15 <command><![CDATA[
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
16 #for $input_classification in $classification:
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
17 ln -s "${input_classification}" "${input_classification.element_identifier}" &&
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
18 #end for
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
19
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
20 export KRAKEN_DB_PATH='${kraken_database.fields.path}' &&
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
21 python '${__tool_directory__}/kraken_taxonomy_report.py'
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
22
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
23 --db '${kraken_database.fields.name}'
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
24 ${show_zeros_param}
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
25 ${header_line_param}
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
26 ${otu_name}
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
27 ${taxo}
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
28 ${rank}
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
29 ${intermediate_rank}
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
30 ${sanitize_names_param}
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
31 #if str( $cluster.cluster_param ):
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
32 --cluster ${cluster.cluster_param}
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
33 #else:
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
34 ${cluster.summ}
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
35 #end if
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
36
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
37 --output '${output_report}'
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
38
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
39 #if $output_tree:
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
40 --output-tree '${output_tree}'
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
41 #end if
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
42
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
43 #for $input_classification in $classification:
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
44 '${input_classification.element_identifier}'
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
45 #end for
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
46 ]]></command>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
47 <inputs>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
48 <param format="tabular" label="Kraken output" multiple="True" name="classification" type="data" />
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
49 <param checked="False" falsevalue="" argument="--show-zeros" label="Display taxa even if they lack a read in any sample" name="show_zeros_param" truevalue="--show-zeros" type="boolean" />
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
50 <param checked="True" falsevalue="" argument="--header-line" label="Display a header line indicating sample IDs" name="header_line_param" truevalue="--header-line" type="boolean" />
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
51 <param label="Select a Kraken database" name="kraken_database" type="select" help="Select the same database used to classify reads">
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
52 <options from_data_table="kraken_databases">
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
53 <validator message="No Kraken databases are available" type="no_options" />
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
54 </options>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
55 </param>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
56 <param label="How to name OTUs" name="otu_name" type="select" multiple="False">
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
57 <option value="" selected="True">Node name only</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
58 <option value="--name-long">Taxonified Name</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
59 <option value="--name-id">Node ID</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
60 </param>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
61 <param checked="True" falsevalue="" argument="--sanitize-names" label="Sanitize Names" name="sanitize_names_param" truevalue="--sanitize-names" type="boolean" help="Replace special chars (\t| |\||\.;) with underscore (_)" />
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
62 <param checked="False" falsevalue="" argument="--show-rank" label="Output Rank Name in (second to) last column" name="rank" truevalue="--show-rank" type="boolean" />
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
63 <param checked="False" falsevalue="" argument="--taxonomy" label="Output taxonomy in last column" name="taxo" truevalue="--taxonomy" type="boolean" />
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
64 <param checked="True" falsevalue="" argument="--intermediate" label="Display intermediate ranks" name="intermediate_rank" truevalue="--intermediate" type="boolean" />
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
65 <conditional name="cluster">
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
66 <param argument="--cluster" help="Combines rows under the selected taxon and reports only selected rank." label="Cluster by taxonomic rank" name="cluster_param" type="select">
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
67 <option value="Superkingdom">Superkingdom</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
68 <option value="Kingdom">Kingdom</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
69 <option value="Subkingdom">Subkingdom</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
70 <option value="Superphylum">Superphylum</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
71 <option value="Phylum">Phylum</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
72 <option value="Subphylum">Subphylum</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
73 <option value="Superclass">Superclass</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
74 <option value="Class">Class</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
75 <option value="Subclass">Subclass</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
76 <option value="Infraclass">Infraclass</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
77 <option value="Superorder">Superorder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
78 <option value="Order">Order</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
79 <option value="Suborder">Suborder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
80 <option value="Infraorder">infraorder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
81 <option value="Parvorder">Parvorder</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
82 <option value="Superfamily">Superfamily</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
83 <option value="Family">Family</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
84 <option value="Subfamily">Subfamily</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
85 <option value="Tribe">Tribe</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
86 <option value="Subtribe">Subtribe</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
87 <option value="Genus">Genus</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
88 <option value="Subgenus">Subgenus</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
89 <option value="Species Group">Species Group</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
90 <option value="Species Subgroup">Species Subgroup</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
91 <option value="Species">Species</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
92 <option value="Subspecies">Subspecies</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
93 <option value="Varietas">Varietas</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
94 <option value="Forma">Forma</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
95 <option value="" selected="True">No Clustering</option>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
96 </param>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
97 <when value="">
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
98 <param checked="False" falsevalue="" argument="--summation" label="Summation of lower ranks into higher ranks" name="summ" truevalue="--summation" type="boolean" />
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
99 </when>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
100 <when value="Superkingdom"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
101 <when value="Kingdom"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
102 <when value="Subkingdom"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
103 <when value="Superphylum"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
104 <when value="Phylum"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
105 <when value="Subphylum"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
106 <when value="Superclass"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
107 <when value="Class"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
108 <when value="Subclass"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
109 <when value="Infraclass"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
110 <when value="Superorder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
111 <when value="Order"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
112 <when value="Suborder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
113 <when value="Infraorder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
114 <when value="Parvorder"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
115 <when value="Superfamily"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
116 <when value="Family"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
117 <when value="Subfamily"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
118 <when value="Tribe"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
119 <when value="Subtribe"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
120 <when value="Genus"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
121 <when value="Subgenus"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
122 <when value="Species Group"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
123 <when value="Species Subgroup"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
124 <when value="Species"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
125 <when value="Subspecies"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
126 <when value="Varietas"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
127 <when value="Forma"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
128 </conditional>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
129 <param checked="False" falsevalue="" label="Output a newick tree" name="tree" truevalue="true" type="boolean" help="Trees are pruned at specified rank when clustering"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
130 </inputs>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
131 <outputs>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
132 <data format="tabular" name="output_report" label="${tool.name} on ${on_string} (Abundances)"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
133 <data format="txt" name="output_tree" label="${tool.name} on ${on_string} (Newick Tree)">
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
134 <filter>tree</filter>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
135 </data>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
136 </outputs>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
137 <tests>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
138 <test expect_num_outputs="2">
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
139 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
140 <param name="show_zeros_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
141 <param name="header_line_param" value="True"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
142 <param name="kraken_database" value="test_db"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
143 <param name="otu_name" value=""/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
144 <param name="sanitize_names_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
145 <param name="rank" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
146 <param name="taxo" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
147 <param name="intermediate_rank" value="True"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
148 <conditional name="cluster">
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
149 <param name="cluster_param" value=""/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
150 <param name="summ" value="True"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
151 </conditional>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
152 <param name="tree" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
153 <output name="output_report" file="output_abundance_1.tabular" ftype="tabular"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
154 <output name="output_tree" file="output_tree_1.newick" />
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
155 </test>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
156 <test expect_num_outputs="2">
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
157 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
158 <param name="show_zeros_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
159 <param name="header_line_param" value="True"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
160 <param name="kraken_database" value="test_db"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
161 <param name="otu_name" value=""/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
162 <param name="sanitize_names_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
163 <param name="rank" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
164 <param name="taxo" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
165 <param name="intermediate_rank" value="True"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
166 <conditional name="cluster">
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
167 <param name="cluster_param" value=""/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
168 <param name="summ" value="False"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
169 </conditional>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
170 <param name="tree" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
171 <output name="output_report" file="output_abundance_2.tabular" ftype="tabular"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
172 <output name="output_tree" file="output_tree_1.newick" />
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
173 </test>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
174 <test expect_num_outputs="2">
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
175 <param name="classification" value="input_kraken_1.tabular" ftype="tabular"/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
176 <param name="show_zeros_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
177 <param name="header_line_param" value="True"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
178 <param name="kraken_database" value="test_db"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
179 <param name="otu_name" value=""/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
180 <param name="sanitize_names_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
181 <param name="rank" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
182 <param name="taxo" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
183 <param name="intermediate_rank" value="False"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
184 <conditional name="cluster">
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
185 <param name="cluster_param" value="Species"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
186 </conditional>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
187 <param name="tree" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
188 <output name="output_report" file="output_abundance_3.tabular" ftype="tabular"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
189 <output name="output_tree" file="output_tree_3.newick" />
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
190 </test>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
191 <test expect_num_outputs="2">
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
192 <param name="classification" value="input_kraken_1.tabular,input_kraken_2.tabular" ftype="tabular"/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
193 <param name="show_zeros_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
194 <param name="header_line_param" value="True"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
195 <param name="kraken_database" value="test_db"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
196 <param name="otu_name" value=""/>
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
197 <param name="sanitize_names_param" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
198 <param name="rank" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
199 <param name="taxo" value="True"/>
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
200 <param name="intermediate_rank" value="False"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
201 <conditional name="cluster">
5
bfae8da6082c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 5b5fa1a3d9492fbbf01aa6ddceca9d4525c7cba5
iuc
parents: 4
diff changeset
202 <param name="cluster_param" value="Species"/>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
203 </conditional>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
204 <param name="tree" value="True"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
205 <output name="output_report" file="output_abundance_4.tabular" ftype="tabular"/>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
206 <output name="output_tree" file="output_tree_3.newick" />
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
207 </test>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
208 </tests>
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
209 <help><![CDATA[
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
210 .. class:: warningmark
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
211
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
212 **Note**: the database used must be the same as the one used in the original Kraken run
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
213
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
214 -----
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
215
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
216 **What is Does**
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
217
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
218 Summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple experiments, conditions, locations, etc.
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
219
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
220 -----
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
221
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
222 **Output**
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
223
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
224 The output is tab-delimited, with one line per taxon.
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
225
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
226 Will optionally output a newick tree built from the kraken database taxonomy using the specified options. Tree branch lengths will be set to "1.00000".
2
528a1d91b066 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
iuc
parents: 1
diff changeset
227 ]]></help>
0
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
228 <citations>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
229 <citation type="bibtex">@unpublished{Kraken-Taxonomy-Report:2016,
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
230 title = "Kraken Taxonomy Report",
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
231 author = "Daniel Blankenberg",
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
232 url = "https://github.com/blankenberg/Kraken-Taxonomy-Report",
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
233 year = "2016 (accessed June 1, 2016)"
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
234 }</citation>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
235 </citations>
3f1a0d47ea8d planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/kraken_taxonomy_report/ commit 1c0a7aff7c5f6578a11e6e8e9bface8d02e7f8a1
iuc
parents:
diff changeset
236 </tool>