Mercurial > repos > iuc > qiime_filter_fasta
comparison filter_fasta.xml @ 0:794553858db3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author | iuc |
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date | Thu, 18 May 2017 09:38:13 -0400 |
parents | |
children | 82ab467a74fc |
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-1:000000000000 | 0:794553858db3 |
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1 <tool id="qiime_filter_fasta" name="Filter fasta" version="@WRAPPER_VERSION@.0"> | |
2 <description>to remove sequences based on input criteria</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command detect_errors="aggressive"><![CDATA[ | |
8 filter_fasta.py | |
9 --input_fasta_fp '$input_fasta_fp' | |
10 --output_fasta_fp '$fitered_fasta' | |
11 #if $selection.type == "otu_map" | |
12 --otu_map '$selection.otu_map' | |
13 #else if $selection.type == "seq_list" | |
14 --seq_id_fp '$selection.seq_id_fp' | |
15 #else if $selection.type == "biom" | |
16 --biom_fp '$selection.biom_fp' | |
17 #else if $selection.type == "fasta" | |
18 --subject_fasta_fp '$selection.subject_fasta_fp' | |
19 #else if $selection.type == "prefix" | |
20 --seq_id_prefix '$selection.seq_id_prefix' | |
21 #else if $selection.type == "prefix_list" | |
22 --sample_id_fp '$selection.sample_id_fp' | |
23 #else if $selection.type == "valid_states" | |
24 --mapping_fp '$selection.mapping_fp' | |
25 --valid_states '$selection.valid_states' | |
26 #end if | |
27 $negate | |
28 ]]></command> | |
29 <inputs> | |
30 <param name="input_fasta_fp" argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/> | |
31 <conditional name="selection"> | |
32 <param name="type" label="Type of criteria for filtering" type="select"> | |
33 <option value="otu_map">OTU map-based filtering</option> | |
34 <option value="seq_list">Filtering using a list of sequence identifiers</option> | |
35 <option value="biom">Filtering based on OTU identifiers in a BIOM file</option> | |
36 <option value="fasta">Filtering based on sequence identifiers in a Fasta file</option> | |
37 <option value="prefix">Filtering based on a sequence id prefix</option> | |
38 <option value="prefix_list">Filtering based on a list of sequence id prefix</option> | |
39 <option value="valid_states">Filtering based on a sample id description</option> | |
40 </param> | |
41 <when value="otu_map"> | |
42 <param argument="--otu_map" type="data" format="txt" label="OTU map where sequences ids are those which should be retained"/> | |
43 </when> | |
44 <when value="seq_list"> | |
45 <param argument="--seq_id_fp" type="data" format="tabular,tsv,csv,txt" label="List of sequence identifiers (or tab-delimited lines with a seq identifier in the first field) which should be retained"/> | |
46 </when> | |
47 <when value="biom"> | |
48 <param argument="--biom_fp" type="data" format="biom1" label="Biom file with OTU identifiers that should be retained"/> | |
49 </when> | |
50 <when value="fasta"> | |
51 <param argument="--subject_fasta_fp" type="data" format="fasta" label="Fasta file where the seq ids should be retained"/> | |
52 </when> | |
53 <when value="prefix"> | |
54 <param argument="--seq_id_prefix" type="text" label="Prefix to keep seqs where seq_id starts with this prefix"/> | |
55 </when> | |
56 <when value="prefix_list"> | |
57 <param argument="--sample_id_fp" type="data" format="txt" label="List of prefix to keep seqs where seq_id starts with a sample id listed in this file"/> | |
58 </when> | |
59 <when value="valid_states"> | |
60 <param argument="--mapping_fp" type="data" format="txt" label="Mapping file"/> | |
61 <param argument="--valid_states" type="text" label="Description of the sample ids to retain"/> | |
62 </when> | |
63 </conditional> | |
64 <param argument="--negate" type="boolean" truevalue="--negate" falsevalue="" checked="False" label="Discard passed seq ids rather than keep passed seq ids?"/> | |
65 </inputs> | |
66 <outputs> | |
67 <data name="fitered_fasta" format="fasta" label="${tool.name} on ${on_string}: Filtered sequences"/> | |
68 </outputs> | |
69 <tests> | |
70 <test> | |
71 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> | |
72 <param name="type" value="otu_map"/> | |
73 <param name="otu_map" value="filter_fasta/otu_map.txt"/> | |
74 <param name="negate" value=""/> | |
75 <output name="fitered_fasta" md5="9185f3cdcba8bcaf159cc3f1fdbb5ebb"/> | |
76 </test> | |
77 <test> | |
78 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> | |
79 <param name="type" value="otu_map"/> | |
80 <param name="otu_map" value="filter_fasta/otu_map.txt"/> | |
81 <param name="negate" value="--negate"/> | |
82 <output name="fitered_fasta" md5="206a5c83e5abbd674f632da73ec518a2"/> | |
83 </test> | |
84 <test> | |
85 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> | |
86 <param name="type" value="seq_list"/> | |
87 <param name="seq_id_fp" value="filter_fasta/seqs_to_keep.txt"/> | |
88 <param name="negate" value=""/> | |
89 <output name="fitered_fasta" md5="19ba95928ca9419f671810240120c8cd"/> | |
90 </test> | |
91 <test> | |
92 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> | |
93 <param name="type" value="biom"/> | |
94 <param name="biom_fp" value="filter_fasta/otu_table.biom"/> | |
95 <param name="negate" value=""/> | |
96 <output name="fitered_fasta" md5="d41d8cd98f00b204e9800998ecf8427e"/> | |
97 </test> | |
98 <test> | |
99 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> | |
100 <param name="type" value="fasta"/> | |
101 <param name="subject_fasta_fp" value="filter_fasta/sl_inseqs.fasta"/> | |
102 <param name="negate" value=""/> | |
103 <output name="fitered_fasta" md5="9c5f416e94bcfb2d4003ea002cbaf617"/> | |
104 </test> | |
105 <test> | |
106 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> | |
107 <param name="type" value="prefix"/> | |
108 <param name="seq_id_prefix" value="S5"/> | |
109 <param name="negate" value=""/> | |
110 <output name="fitered_fasta" md5="c1f2d8c5844733f30ca07547846c4d36"/> | |
111 </test> | |
112 <test> | |
113 <param name="input_fasta_fp" value="filter_fasta/inseqs.fasta"/> | |
114 <param name="type" value="prefix_list"/> | |
115 <param name="sample_id_fp" value="filter_fasta/map.txt"/> | |
116 <param name="negate" value=""/> | |
117 <output name="fitered_fasta" md5="8f0025b067d22ed708ee55de10016785"/> | |
118 </test> | |
119 </tests> | |
120 <help><![CDATA[ | |
121 **What it does** | |
122 | |
123 Filter fasta or fastq file to remove sequences based on input criteria | |
124 ]]></help> | |
125 <citations> | |
126 <expand macro="citations"/> | |
127 </citations> | |
128 </tool> |