Mercurial > repos > galaxyp > filter_by_fasta_ids
comparison filter_by_fasta_ids.xml @ 2:1bd985f14938 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 2bc87e917c91a3b7a43996a0f3752b8992c0c749
author | galaxyp |
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date | Sat, 28 Apr 2018 03:49:28 -0400 |
parents | 8d15aebf55fd |
children | 3c623e81be77 |
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1:8d15aebf55fd | 2:1bd985f14938 |
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1 <tool id="filter_by_fasta_ids" version="1.0" name="Filter by FASTA IDs"> | 1 <tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.0"> |
2 <description>Extract sequences from a FASTA file based on a list of IDs</description> | 2 <description>on the headers and/or the sequences</description> |
3 <command> | 3 <macros> |
4 <![CDATA[ | 4 <xml name="regexp_macro" token_label="Regular expression pattern"> |
5 python $__tool_directory__/filter_by_fasta_ids.py | 5 <param name="regexp" type="text" value="" label="@LABEL@" help="Use the Python regular expression syntax as specified in https://docs.python.org/3/library/re.html"> |
6 $dedup | 6 <validator type="empty_field" /> |
7 '$identifiers' | 7 <sanitizer> |
8 '$input' | 8 <valid initial="string.printable"> |
9 '$output' | 9 <remove value="'"/> |
10 ]]> | 10 </valid> |
11 </command> | 11 <mapping initial="none"> |
12 <add source="'" target="'"'"'" /> | |
13 </mapping> | |
14 </sanitizer> | |
15 </param> | |
16 </xml> | |
17 </macros> | |
18 <requirements> | |
19 <requirement type="package" version="3.6.5">python</requirement> | |
20 </requirements> | |
21 <command><![CDATA[ | |
22 python '$__tool_directory__/filter_by_fasta_ids.py' | |
23 -i '$input' | |
24 #if $header_criteria.header_criteria_select == 'id_list' | |
25 --id_list '$header_criteria.identifiers' | |
26 #elif $header_criteria.header_criteria_select == 'regexp' | |
27 --header_regexp '$header_criteria.regexp' | |
28 #end if | |
29 #if $sequence_criteria.sequence_criteria_select == 'seq_length' | |
30 --min_length $sequence_criteria.min_length | |
31 #if str($sequence_criteria.max_length) | |
32 --max_length $sequence_criteria.max_length | |
33 #end if | |
34 #elif $sequence_criteria.sequence_criteria_select == 'regexp' | |
35 --sequence_regexp '$sequence_criteria.regexp' | |
36 #end if | |
37 $dedup | |
38 -o '$output' | |
39 #if $output_discarded | |
40 -d '$discarded' | |
41 #end if | |
42 ]]></command> | |
12 <inputs> | 43 <inputs> |
13 <param format="fasta" name="input" type="data" label="FASTA sequences"/> | 44 <param name="input" type="data" format="fasta" label="FASTA sequences"/> |
14 <param format="txt" name="identifiers" type="data" label="List of IDs to extract sequences for"/> | 45 <conditional name="header_criteria"> |
15 <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" checked="true" label="Remove duplicate sequences" /> | 46 <param name="header_criteria_select" type="select" label="Criteria for filtering on the headers"> |
47 <option value="">No filtering</option> | |
48 <option value="id_list">List of IDs</option> | |
49 <option value="regexp">Regular expression on the headers</option> | |
50 </param> | |
51 <when value="" /> | |
52 <when value="id_list"> | |
53 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/> | |
54 </when> | |
55 <when value="regexp"> | |
56 <expand macro="regexp_macro" label="Regular expression pattern the header should match" /> | |
57 </when> | |
58 </conditional> | |
59 <conditional name="sequence_criteria"> | |
60 <param name="sequence_criteria_select" type="select" label="Criteria for filtering on the sequences"> | |
61 <option value="">No filtering</option> | |
62 <option value="seq_length">Sequence length</option> | |
63 <option value="regexp">Regular expression on the sequences</option> | |
64 </param> | |
65 <when value="" /> | |
66 <when value="seq_length"> | |
67 <param name="min_length" type="integer" value="0" label="Minimum length" /> | |
68 <param name="max_length" type="integer" min="1" value="" optional="true" label="Maximum length" /> | |
69 </when> | |
70 <when value="regexp"> | |
71 <expand macro="regexp_macro" label="Regular expression pattern the sequence should match" /> | |
72 </when> | |
73 </conditional> | |
74 <param name="dedup" type="boolean" truevalue="--dedup" falsevalue="" label="Remove duplicate sequences" /> | |
75 <param name="output_discarded" type="boolean" label="Output discarded FASTA entries" /> | |
16 </inputs> | 76 </inputs> |
17 <outputs> | 77 <outputs> |
18 <data format="fasta" name="output" label="FASTA sequences for ${identifiers.name}"/> | 78 <data name="output" format="fasta" label="${tool.name} on ${on_string}: FASTA sequences"/> |
79 <data name="discarded" format="fasta" label="${tool.name} on ${on_string}: discarded entries"> | |
80 <filter>output_discarded</filter> | |
81 </data> | |
19 </outputs> | 82 </outputs> |
20 <tests> | 83 <tests> |
21 <test> | 84 <test expect_num_outputs="1"> |
22 <param name="input" ftype="fasta" value="input.fasta" /> | 85 <param name="input" ftype="fasta" value="input.fasta" /> |
86 <param name="header_criteria_select" value="id_list" /> | |
23 <param name="identifiers" ftype="txt" value="ids.txt" /> | 87 <param name="identifiers" ftype="txt" value="ids.txt" /> |
88 <param name="dedup" value="True" /> | |
24 <output name="output" file="output_dedup.fasta" /> | 89 <output name="output" file="output_dedup.fasta" /> |
25 </test> | 90 </test> |
26 <test> | 91 <test expect_num_outputs="2"> |
27 <param name="input" ftype="fasta" value="input.fasta" /> | 92 <param name="input" ftype="fasta" value="input.fasta" /> |
93 <param name="header_criteria_select" value="id_list" /> | |
28 <param name="identifiers" ftype="txt" value="ids.txt" /> | 94 <param name="identifiers" ftype="txt" value="ids.txt" /> |
29 <param name="dedup" value="False" /> | 95 <param name="dedup" value="False" /> |
96 <param name="output_discarded" value="True" /> | |
30 <output name="output" file="output_not_dedup.fasta" /> | 97 <output name="output" file="output_not_dedup.fasta" /> |
98 <output name="discarded" file="discarded_not_dedup.fasta" /> | |
99 </test> | |
100 <test expect_num_outputs="2"> | |
101 <param name="input" ftype="fasta" value="input.fasta" /> | |
102 <param name="header_criteria_select" value="regexp" /> | |
103 <param name="regexp" value="2" /> | |
104 <param name="dedup" value="False" /> | |
105 <param name="output_discarded" value="True" /> | |
106 <output name="output" file="output_header_regexp.fasta" /> | |
107 <output name="discarded" file="discarded_header_regexp.fasta" /> | |
108 </test> | |
109 <test expect_num_outputs="2"> | |
110 <param name="input" ftype="fasta" value="input.fasta" /> | |
111 <param name="sequence_criteria_select" value="seq_length" /> | |
112 <param name="min_length" value="5" /> | |
113 <param name="dedup" value="False" /> | |
114 <param name="output_discarded" value="True" /> | |
115 <output name="output" file="output_min_length5.fasta" /> | |
116 <output name="discarded" file="discarded_min_length5.fasta" /> | |
117 </test> | |
118 <test expect_num_outputs="2"> | |
119 <param name="input" ftype="fasta" value="input.fasta" /> | |
120 <param name="sequence_criteria_select" value="seq_length" /> | |
121 <param name="max_length" value="4" /> | |
122 <param name="dedup" value="False" /> | |
123 <param name="output_discarded" value="True" /> | |
124 <output name="output" file="output_max_length4.fasta" /> | |
125 <output name="discarded" file="discarded_max_length4.fasta" /> | |
126 </test> | |
127 <test expect_num_outputs="2"> | |
128 <param name="input" ftype="fasta" value="input.fasta" /> | |
129 <param name="sequence_criteria_select" value="regexp" /> | |
130 <param name="regexp" value="T{2,}" /> | |
131 <param name="dedup" value="False" /> | |
132 <param name="output_discarded" value="True" /> | |
133 <output name="output" file="output_sequence_regexp.fasta" /> | |
134 <output name="discarded" file="discarded_sequence_regexp.fasta" /> | |
31 </test> | 135 </test> |
32 </tests> | 136 </tests> |
33 <help> | 137 <help><![CDATA[ |
34 <![CDATA[ | |
35 **What it does** | 138 **What it does** |
36 | 139 |
37 Extract sequences from a FASTA file based on a list of IDs. | 140 Filter entries of a FASTA file on the headers and/or the sequences based on various criteria. |
38 ]]> | 141 ]]></help> |
39 </help> | |
40 </tool> | 142 </tool> |