Mercurial > repos > galaxyp > filter_by_fasta_ids
comparison filter_by_fasta_ids.xml @ 4:cd22452edec2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
author | galaxyp |
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date | Thu, 18 Apr 2019 02:45:18 -0400 |
parents | 3c623e81be77 |
children | dff7df6fcab5 |
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3:3c623e81be77 | 4:cd22452edec2 |
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1 <tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.1"> | 1 <tool id="filter_by_fasta_ids" name="Filter FASTA" version="2.2"> |
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" /> |
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': | 26 #if $header_criteria.id_regex.find == 'pattern': |
27 --pattern '$header_criteria.id_regex.pattern' | 27 --pattern '$header_criteria.id_regex.pattern' |
28 #elif $header_criteria.id_regex.find == 'beginning': | 28 #else: |
29 --pattern '$header_criteria.id_regex.pattern' | 29 --pattern '>([^| ]+)' |
30 #end if | 30 #end if |
31 #elif $header_criteria.header_criteria_select == 'regexp' | 31 #elif $header_criteria.header_criteria_select == 'regexp' |
32 --header_regexp '$header_criteria.regexp' | 32 --header_regexp '$header_criteria.regexp' |
33 #end if | 33 #end if |
34 #if $sequence_criteria.sequence_criteria_select == 'seq_length' | 34 #if $sequence_criteria.sequence_criteria_select == 'seq_length' |
54 <option value="regexp">Regular expression on the headers</option> | 54 <option value="regexp">Regular expression on the headers</option> |
55 </param> | 55 </param> |
56 <when value="" /> | 56 <when value="" /> |
57 <when value="id_list"> | 57 <when value="id_list"> |
58 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/> | 58 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/> |
59 | |
60 | |
61 <conditional name="id_regex"> | 59 <conditional name="id_regex"> |
62 <param name="find" type="select" label="Match IDs by"> | 60 <param name="find" type="select" label="Match IDs by" |
61 help="Default: >ID will use search pattern >([^| ]+) to input ID; Use custom regex to change"> | |
63 <option value="beginning">Default: ID is expected at the beginning: >ID </option> | 62 <option value="beginning">Default: ID is expected at the beginning: >ID </option> |
64 <help>Default: >ID will use search pattern >([^| ]+) to input ID; Use custom regex to change</help> | |
65 <option value="pattern">Custom regex pattern</option> | 63 <option value="pattern">Custom regex pattern</option> |
66 </param> | 64 </param> |
67 <when value="beginning"> | 65 <when value="beginning" /> |
68 <param name="pattern" type="hidden" value=">([^| ]+)" label="regex search pattern for ID" > | |
69 <sanitizer sanitize="False"/> | |
70 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator> | |
71 </param> | |
72 </when> | |
73 <when value="pattern"> | 66 <when value="pattern"> |
74 <param name="pattern" type="text" value="" label="regex search pattern for ID"> | 67 <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> | 68 help="Search pattern must contain %s where the ID will be substituted. Use this for Uniprot Acc: >.+?\|(.+?)\|.*$"> |
76 <sanitizer sanitize="False"/> | 69 <sanitizer sanitize="False"/> |
77 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator> | 70 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</validator> |
78 </param> | 71 </param> |
79 </when> | 72 </when> |
80 </conditional> | 73 </conditional> |
81 | |
82 | |
83 </when> | 74 </when> |
84 <when value="regexp"> | 75 <when value="regexp"> |
85 <expand macro="regexp_macro" label="Regular expression pattern the header should match" /> | 76 <expand macro="regexp_macro" label="Regular expression pattern the header should match" /> |
86 </when> | 77 </when> |
87 </conditional> | 78 </conditional> |
135 <output name="output" file="output_not_dedup.fasta" /> | 126 <output name="output" file="output_not_dedup.fasta" /> |
136 <output name="discarded" file="discarded_not_dedup.fasta" /> | 127 <output name="discarded" file="discarded_not_dedup.fasta" /> |
137 </test> | 128 </test> |
138 <test expect_num_outputs="2"> | 129 <test expect_num_outputs="2"> |
139 <param name="input" ftype="fasta" value="input.fasta" /> | 130 <param name="input" ftype="fasta" value="input.fasta" /> |
140 <param name="header_criteria_select" value="regexp" /> | 131 <conditional name="header_criteria"> |
141 <param name="regexp" value="2" /> | 132 <param name="header_criteria_select" value="regexp" /> |
133 <param name="regexp" value="2" /> | |
134 </conditional> | |
142 <param name="dedup" value="False" /> | 135 <param name="dedup" value="False" /> |
143 <param name="output_discarded" value="True" /> | 136 <param name="output_discarded" value="True" /> |
144 <output name="output" file="output_header_regexp.fasta" /> | 137 <output name="output" file="output_header_regexp.fasta" /> |
145 <output name="discarded" file="discarded_header_regexp.fasta" /> | 138 <output name="discarded" file="discarded_header_regexp.fasta" /> |
146 </test> | 139 </test> |
162 <output name="output" file="output_max_length4.fasta" /> | 155 <output name="output" file="output_max_length4.fasta" /> |
163 <output name="discarded" file="discarded_max_length4.fasta" /> | 156 <output name="discarded" file="discarded_max_length4.fasta" /> |
164 </test> | 157 </test> |
165 <test expect_num_outputs="2"> | 158 <test expect_num_outputs="2"> |
166 <param name="input" ftype="fasta" value="input.fasta" /> | 159 <param name="input" ftype="fasta" value="input.fasta" /> |
167 <param name="sequence_criteria_select" value="regexp" /> | 160 <conditional name="sequence_criteria"> |
168 <param name="regexp" value="T{2,}" /> | 161 <param name="sequence_criteria_select" value="regexp" /> |
162 <param name="regexp" value="T{2,}" /> | |
163 </conditional> | |
169 <param name="dedup" value="False" /> | 164 <param name="dedup" value="False" /> |
170 <param name="output_discarded" value="True" /> | 165 <param name="output_discarded" value="True" /> |
171 <output name="output" file="output_sequence_regexp.fasta" /> | 166 <output name="output" file="output_sequence_regexp.fasta" /> |
172 <output name="discarded" file="discarded_sequence_regexp.fasta" /> | 167 <output name="discarded" file="discarded_sequence_regexp.fasta" /> |
168 </test> | |
169 <test expect_num_outputs="2"> | |
170 <param name="input" ftype="fasta" value="input.fasta" /> | |
171 <conditional name="header_criteria"> | |
172 <param name="header_criteria_select" value="regexp" /> | |
173 <param name="regexp" value="3|5" /> | |
174 </conditional> | |
175 <conditional name="sequence_criteria"> | |
176 <param name="sequence_criteria_select" value="regexp" /> | |
177 <param name="regexp" value="ACGT" /> | |
178 </conditional> | |
179 <param name="dedup" value="False" /> | |
180 <param name="output_discarded" value="True" /> | |
181 <output name="output" file="output_header_regexp_sequence_regexp.fasta" /> | |
182 <output name="discarded" file="discarded_header_regexp_sequence_regexp.fasta" /> | |
173 </test> | 183 </test> |
174 </tests> | 184 </tests> |
175 <help><![CDATA[ | 185 <help><![CDATA[ |
176 **What it does** | 186 **What it does** |
177 | 187 |