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comparison pick_rep_set.xml @ 0:6ebade612aa0 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 09:32:11 -0400
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children 8218f848c2b9
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1 <tool id="qiime_pick_rep_set" name="Pick representative set of sequences" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>pick_rep_set.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[
9 pick_rep_set.py
10 --input_file '$input_file'
11 #if $picking.type == "de_novo"
12 --fasta_file '$picking.fasta_file'
13 #else if $picking.type == "preferred"
14 --reference_seqs_fp '$picking.reference_seqs_fp'
15 #if $picking.fasta_file
16 --fasta_file '$picking.fasta_file'
17 #end if
18 #end if
19 --rep_set_picking_method '$rep_set_picking_method'
20 --sort_by '$sort_by'
21 --result_fp '$result_fp'
22 --log_fp '$log_fp'
23 ]]></command>
24 <inputs>
25 <param argument="--input_file" type="data" format="txt" label="Input OTU mapping file"/>
26 <conditional name="picking">
27 <param name="type" type="select" label="Type of OTU picking">
28 <option value="de_novo">Picking a representative set for de novo-picked OTUs</option>
29 <option value="preferred">Picking OTUs with "preferred representative" sequence</option>
30 </param>
31 <when value="de_novo">
32 <param argument="--fasta_file" type="data" format="fasta" label="Input fasta file with all of the sequences whose identifiers are listed in the OTU map"/>
33 </when>
34 <when value="preferred">
35 <param argument="--reference_seqs_fp" type="data" format="fasta" label="Collection of preferred representative sequences "/>
36 <param argument="--fasta_file" type="data" format="fasta" optional="True" label="Input fasta file with all of the sequences whose identifiers are listed in the OTU map" help="If new clusters were allowed"/>
37 </when>
38 </conditional>
39 <param argument="--rep_set_picking_method" type="select" label="Method for picking representative sets">
40 <option value="random">random</option>
41 <option value="longest">longest</option>
42 <option value="most_abundant">most_abundant</option>
43 <option value="first" selected="true">first (chooses cluster seed when picking otus with uclust)</option>
44 </param>
45 <param argument="--sort_by" type="select" label="Sorting by">
46 <option value="otu" selected="true">OTU</option>
47 <option value="seq_id">Sequence id</option>
48 </param>
49 </inputs>
50 <outputs>
51 <data format="fasta" name="result_fp" label="${tool.name} on ${on_string}: Representative sequences"/>
52 <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: Log"/>
53 </outputs>
54 <tests>
55 <test>
56 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
57 <param name="type" value="de_novo"/>
58 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
59 <param name="rep_set_picking_method" value="first"/>
60 <param name="sort_by" value="otu"/>
61 <output name="result_fp" file="pick_rep_set/first_otu_fasta.fasta"/>
62 <output name="log_fp">
63 <assert_contents>
64 <has_text text="GenericRepSetPicker"/>
65 <has_text text="Algorithm:first"/>
66 </assert_contents>
67 </output>
68 </test>
69 <test>
70 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
71 <param name="type" value="preferred"/>
72 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
73 <param name="reference_seqs_fp" value="pick_rep_set/refseqs.fasta"/>
74 <param name="rep_set_picking_method" value="first"/>
75 <param name="sort_by" value="otu"/>
76 <output name="result_fp" file="pick_rep_set/first_otu_fasta_ref.fasta"/>
77 <output name="log_fp">
78 <assert_contents>
79 <has_text text="ReferenceRepSetPicker"/>
80 <has_text text="Algorithm:first"/>
81 </assert_contents>
82 </output>
83 </test>
84 <test>
85 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
86 <param name="type" value="de_novo"/>
87 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
88 <param name="rep_set_picking_method" value="longest"/>
89 <param name="sort_by" value="otu"/>
90 <output name="result_fp" file="pick_rep_set/longest_otu_fasta.fasta"/>
91 <output name="log_fp">
92 <assert_contents>
93 <has_text text="GenericRepSetPicker"/>
94 <has_text text="Algorithm:longest"/>
95 </assert_contents>
96 </output>
97 </test>
98 <test>
99 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
100 <param name="type" value="de_novo"/>
101 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
102 <param name="rep_set_picking_method" value="most_abundant"/>
103 <param name="sort_by" value="otu"/>
104 <output name="result_fp" file="pick_rep_set/most_abundant_otu_fasta.fasta"/>
105 <output name="log_fp">
106 <assert_contents>
107 <has_text text="GenericRepSetPicker"/>
108 <has_text text="Algorithm:most_abundant"/>
109 </assert_contents>
110 </output>
111 </test>
112 <test>
113 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
114 <param name="type" value="de_novo"/>
115 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
116 <param name="rep_set_picking_method" value="random"/>
117 <param name="sort_by" value="otu"/>
118 <output name="result_fp">
119 <assert_contents>
120 <has_text text="1 PC.636_263"/>
121 <has_text text="101 PC.634_99"/>
122 </assert_contents>
123 </output>
124 <output name="log_fp">
125 <assert_contents>
126 <has_text text="GenericRepSetPicker"/>
127 <has_text text="Algorithm:random"/>
128 </assert_contents>
129 </output>
130 </test>
131 <test>
132 <param name="input_file" value="pick_rep_set/seqs_otus.txt"/>
133 <param name="type" value="de_novo"/>
134 <param name="fasta_file" value="pick_rep_set/seqs.fna"/>
135 <param name="rep_set_picking_method" value="first"/>
136 <param name="sort_by" value="seq_id"/>
137 <output name="result_fp" file="pick_rep_set/first_seq_id_fasta.fasta"/>
138 <output name="log_fp">
139 <assert_contents>
140 <has_text text="GenericRepSetPicker"/>
141 <has_text text="Algorithm:first"/>
142 </assert_contents>
143 </output>
144 </test>
145 </tests>
146 <help><![CDATA[
147 **What it does**
148
149 After picking OTUs, you can then pick a representative set of sequences. For each OTU, you will end up with one sequence that can be used in subsequent analyses.
150
151 The output from pick_rep_set.py is a single FASTA file containing one sequence per OTU. The FASTA header lines will be the OTU identifier (from here on used as the unique sequence identifier) followed by a space, followed by the sequence identifier originally associated with the representative sequence. The name of the output FASTA file will be <input_sequences_filepath>_rep_set.fasta by default, or can be specified via the "-o" parameter.
152 ]]></help>
153 <citations>
154 <expand macro="citations"/>
155 </citations>
156 </tool>