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comparison pick_closed_reference_otus.xml @ 0:ec9c32b3a462 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:21:57 -0400
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-1:000000000000 0:ec9c32b3a462
1 <tool id="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>