Mercurial > repos > iuc > qiime_pick_closed_reference_otus
comparison pick_closed_reference_otus.xml @ 0:2b6d3067087a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 04:02:18 -0400 |
parents | |
children | 935abbf93f99 |
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-1:000000000000 | 0:2b6d3067087a |
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1 <tool id="qiime_pick_closed_reference_otus" name="Perform closed-reference OTU picking" version="@WRAPPER_VERSION@.0"> | |
2 <description></description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <version_command>pick_closed_reference_otus.py --version</version_command> | |
8 <command detect_errors="aggressive"><![CDATA[ | |
9 pick_closed_reference_otus.py | |
10 --input_fp '$input_fp' | |
11 --output_dir otus | |
12 #if str( $ref_seq.selector ) == 'history' | |
13 #set $ref = $ref_seq.reference_fp | |
14 #else | |
15 #set $ref = $ref_seq.reference_fp.fields.path | |
16 #end if | |
17 --reference_fp '$ref' | |
18 #if str( $taxonomy.selector ) == 'taxonomy_map' | |
19 #if str( $taxonomy.taxo_map.selector ) == 'history' | |
20 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp | |
21 #else | |
22 #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp.fields.path | |
23 #end if | |
24 --taxonomy_fp '$taxonomy' | |
25 #else if str( $taxonomy.selector ) == 'assign_taxonomy' | |
26 --assign_taxonomy | |
27 #else if str( $taxonomy.selector ) == 'suppress_taxonomy_assignment' | |
28 --suppress_taxonomy_assignment | |
29 #end if | |
30 #if $parameter_fp | |
31 --parameter_fp '$parameter_fp' | |
32 #end if | |
33 $parallel | |
34 -O "\${GALAXY_SLOTS:-4}" | |
35 ]]></command> | |
36 <inputs> | |
37 <param argument="--input_fp" type="data" format="fasta" label="Input sequence file"/> | |
38 <conditional name="ref_seq"> | |
39 <param name="selector" type="select" label="Reference sequences to query"> | |
40 <option value="cached" selected="True">Public databases</option> | |
41 <option value="history">Databases from your history</option> | |
42 </param> | |
43 <when value="cached"> | |
44 <param argument="--reference_fp" label="Reference sequences" type="select"> | |
45 <options from_data_table="qiime_rep_set"/> | |
46 </param> | |
47 </when> | |
48 <when value="history"> | |
49 <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/> | |
50 </when> | |
51 </conditional> | |
52 <conditional name="taxonomy"> | |
53 <param name="selector" type="select" label="Assign taxonomy?"> | |
54 <option value="taxonomy_map" selected="True">Assign taxonomy using a taxonomy map</option> | |
55 <option value="assign_taxonomy">Assign taxonomy to each sequence using assign_taxonomy.py</option> | |
56 <option value="suppress_taxonomy_assignment">Skip the taxonomy assignment step</option> | |
57 </param> | |
58 <when value="taxonomy_map"> | |
59 <conditional name="taxo_map"> | |
60 <param name="selector" type="select" label="Taxonomy map to use"> | |
61 <option value="cached" selected="True">Public taxonomy map</option> | |
62 <option value="history">Taxonomy map from your history</option> | |
63 </param> | |
64 <when value="cached"> | |
65 <param argument="--taxonomy_fp" label="Taxonomy map" type="select"> | |
66 <options from_data_table="qiime_taxonomy"/> | |
67 </param> | |
68 </when> | |
69 <when value="history"> | |
70 <param argument="--taxonomy_fp" type="data" format="txt" label="Taxonomy map"/> | |
71 </when> | |
72 </conditional> | |
73 </when> | |
74 <when value="assign_taxonomy"/> | |
75 <when value="suppress_taxonomy_assignment"/> | |
76 </conditional> | |
77 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/> | |
78 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/> | |
79 </inputs> | |
80 <outputs> | |
81 <data name="otu_table" format="biom1" from_work_dir="otus/otu_table.biom" label="${tool.name} on ${on_string}: OTU table"/> | |
82 </outputs> | |
83 <tests> | |
84 <test> | |
85 <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> | |
86 <conditional name="ref_seq"> | |
87 <param name="selector" value="history"/> | |
88 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> | |
89 </conditional> | |
90 <conditional name="taxonomy"> | |
91 <param name="selector" value="taxonomy_map"/> | |
92 <conditional name="taxo_map"> | |
93 <param name="selector" value="history"/> | |
94 <param name="taxonomy_fp" value="pick_closed_reference_otus/taxa.txt"/> | |
95 </conditional> | |
96 </conditional> | |
97 <param name="parallel" value=""/> | |
98 <output name="otu_table" file="pick_closed_reference_otus/basic_otu_table.biom" compare="sim_size" /> | |
99 </test> | |
100 <test> | |
101 <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> | |
102 <conditional name="ref_seq"> | |
103 <param name="selector" value="history"/> | |
104 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> | |
105 </conditional> | |
106 <conditional name="taxonomy"> | |
107 <param name="selector" value="taxonomy_map"/> | |
108 <conditional name="taxo_map"> | |
109 <param name="selector" value="history"/> | |
110 <param name="taxonomy_fp" value="pick_closed_reference_otus/taxa.txt"/> | |
111 </conditional> | |
112 </conditional> | |
113 <param name="parameter_fp" value="pick_closed_reference_otus/sortmerna_params.txt"/> | |
114 <param name="parallel" value=""/> | |
115 <output name="otu_table" file="pick_closed_reference_otus/sortmerna_otu_table.biom" compare="sim_size" /> | |
116 </test> | |
117 <test> | |
118 <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> | |
119 <conditional name="ref_seq"> | |
120 <param name="selector" value="history"/> | |
121 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> | |
122 </conditional> | |
123 <conditional name="taxonomy"> | |
124 <param name="selector" value="assign_taxonomy"/> | |
125 </conditional> | |
126 <param name="parallel" value=""/> | |
127 <output name="otu_table" file="pick_closed_reference_otus/assign_taxonomy_otu_table.biom" compare="sim_size" /> | |
128 </test> | |
129 <test> | |
130 <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> | |
131 <conditional name="ref_seq"> | |
132 <param name="selector" value="history"/> | |
133 <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> | |
134 </conditional> | |
135 <conditional name="taxonomy"> | |
136 <param name="selector" value="suppress_taxonomy_assignment"/> | |
137 </conditional> | |
138 <param name="parallel" value=""/> | |
139 <output name="otu_table" file="pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom" compare="sim_size" /> | |
140 </test> | |
141 </tests> | |
142 <help><![CDATA[ | |
143 **What it does** | |
144 | |
145 This script picks OTUs using a closed reference and constructs an OTU table. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. If full-length genomes are provided as the reference sequences, this script applies the Shotgun UniFrac method. | |
146 | |
147 More information about this tool is available on | |
148 `QIIME documentation <http://qiime.org/scripts/pick_closed_reference_otus.html>`_. | |
149 ]]></help> | |
150 <citations> | |
151 <expand macro="citations"/> | |
152 </citations> | |
153 </tool> |