Mercurial > repos > galaxyp > filter_by_fasta_ids
comparison filter_by_fasta_ids.xml @ 3:3c623e81be77 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 0556e0fe5aa17c84033a75a45baeb3a4c2b5ff76
author | galaxyp |
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date | Fri, 15 Feb 2019 16:38:31 -0500 |
parents | 1bd985f14938 |
children | cd22452edec2 |
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2:1bd985f14938 | 3:3c623e81be77 |
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1 <tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.0"> | 1 <tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.1"> |
2 <description>on the headers and/or the sequences</description> | 2 <description>on the headers and/or the sequences</description> |
3 <macros> | 3 <macros> |
4 <xml name="regexp_macro" token_label="Regular expression pattern"> | 4 <xml name="regexp_macro" token_label="Regular expression pattern"> |
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"> | 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 <validator type="empty_field" /> | 6 <validator type="empty_field" /> |
21 <command><![CDATA[ | 21 <command><![CDATA[ |
22 python '$__tool_directory__/filter_by_fasta_ids.py' | 22 python '$__tool_directory__/filter_by_fasta_ids.py' |
23 -i '$input' | 23 -i '$input' |
24 #if $header_criteria.header_criteria_select == 'id_list' | 24 #if $header_criteria.header_criteria_select == 'id_list' |
25 --id_list '$header_criteria.identifiers' | 25 --id_list '$header_criteria.identifiers' |
26 #if $header_criteria.id_regex.find == 'pattern': | |
27 --pattern '$header_criteria.id_regex.pattern' | |
28 #elif $header_criteria.id_regex.find == 'beginning': | |
29 --pattern '$header_criteria.id_regex.pattern' | |
30 #end if | |
26 #elif $header_criteria.header_criteria_select == 'regexp' | 31 #elif $header_criteria.header_criteria_select == 'regexp' |
27 --header_regexp '$header_criteria.regexp' | 32 --header_regexp '$header_criteria.regexp' |
28 #end if | 33 #end if |
29 #if $sequence_criteria.sequence_criteria_select == 'seq_length' | 34 #if $sequence_criteria.sequence_criteria_select == 'seq_length' |
30 --min_length $sequence_criteria.min_length | 35 --min_length $sequence_criteria.min_length |
49 <option value="regexp">Regular expression on the headers</option> | 54 <option value="regexp">Regular expression on the headers</option> |
50 </param> | 55 </param> |
51 <when value="" /> | 56 <when value="" /> |
52 <when value="id_list"> | 57 <when value="id_list"> |
53 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/> | 58 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/> |
59 | |
60 | |
61 <conditional name="id_regex"> | |
62 <param name="find" type="select" label="Match IDs by"> | |
63 <option value="beginning">Default: ID is expected at the beginning: >ID </option> | |
64 <help>Default: >ID will use search pattern >([^| ]+) to input ID; Use custom regex to change</help> | |
65 <option value="pattern">Custom regex pattern</option> | |
66 </param> | |
67 <when value="beginning"> | |
68 <param name="pattern" type="hidden" value=">([^| ]+)" label="regex search pattern for ID" > | |
69 <sanitizer sanitize="False"/> | |
70 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator> | |
71 </param> | |
72 </when> | |
73 <when value="pattern"> | |
74 <param name="pattern" type="text" value="" label="regex search pattern for ID"> | |
75 <help>search pattern must contain %s where the ID will be substituted. Use this for Uniprot Acc: >.+?\|(.+?)\|.*$ </help> | |
76 <sanitizer sanitize="False"/> | |
77 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator> | |
78 </param> | |
79 </when> | |
80 </conditional> | |
81 | |
82 | |
54 </when> | 83 </when> |
55 <when value="regexp"> | 84 <when value="regexp"> |
56 <expand macro="regexp_macro" label="Regular expression pattern the header should match" /> | 85 <expand macro="regexp_macro" label="Regular expression pattern the header should match" /> |
57 </when> | 86 </when> |
58 </conditional> | 87 </conditional> |
85 <param name="input" ftype="fasta" value="input.fasta" /> | 114 <param name="input" ftype="fasta" value="input.fasta" /> |
86 <param name="header_criteria_select" value="id_list" /> | 115 <param name="header_criteria_select" value="id_list" /> |
87 <param name="identifiers" ftype="txt" value="ids.txt" /> | 116 <param name="identifiers" ftype="txt" value="ids.txt" /> |
88 <param name="dedup" value="True" /> | 117 <param name="dedup" value="True" /> |
89 <output name="output" file="output_dedup.fasta" /> | 118 <output name="output" file="output_dedup.fasta" /> |
119 </test> | |
120 <test expect_num_outputs="1"> | |
121 <param name="input" ftype="fasta" value="input_sp.fasta" /> | |
122 <param name="header_criteria_select" value="id_list" /> | |
123 <param name="find" value="pattern" /> | |
124 <param name="pattern" value=">.+?\|(.+?)\|.*$" /> | |
125 <param name="identifiers" ftype="txt" value="ids_sp.txt" /> | |
126 <param name="dedup" value="True" /> | |
127 <output name="output" file="output_sp_dedup.fasta" /> | |
90 </test> | 128 </test> |
91 <test expect_num_outputs="2"> | 129 <test expect_num_outputs="2"> |
92 <param name="input" ftype="fasta" value="input.fasta" /> | 130 <param name="input" ftype="fasta" value="input.fasta" /> |
93 <param name="header_criteria_select" value="id_list" /> | 131 <param name="header_criteria_select" value="id_list" /> |
94 <param name="identifiers" ftype="txt" value="ids.txt" /> | 132 <param name="identifiers" ftype="txt" value="ids.txt" /> |