Mercurial > repos > galaxyp > filter_by_fasta_ids

comparison filter_by_fasta_ids.xml @ 4:cd22452edec2 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids commit 5e7097242e584763d3a6d86a824ee933500667af
author galaxyp
date Thu, 18 Apr 2019 02:45:18 -0400
parents 3c623e81be77
children dff7df6fcab5
comparison
equal deleted inserted replaced
3:3c623e81be77 4:cd22452edec2
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 $sequence_criteria.sequence_criteria_select == 'seq_length'
54 <option value="regexp">Regular expression on the headers</option> 54 <option value="regexp">Regular expression on the headers</option>
55 </param> 55 </param>
56 <when value="" /> 56 <when value="" />
57 <when value="id_list"> 57 <when value="id_list">
58 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/> 58 <param name="identifiers" type="data" format="txt" label="List of IDs to extract sequences for"/>
59
60
61 <conditional name="id_regex"> 59 <conditional name="id_regex">
62 <param name="find" type="select" label="Match IDs by"> 60 <param name="find" type="select" label="Match IDs by"
61 help="Default: &gt;ID will use search pattern >([^| ]+) to input ID; Use custom regex to change">
63 <option value="beginning">Default: ID is expected at the beginning: &gt;ID </option> 62 <option value="beginning">Default: ID is expected at the beginning: &gt;ID </option>
64 <help>Default: &gt;ID will use search pattern >([^| ]+) to input ID; Use custom regex to change</help>
65 <option value="pattern">Custom regex pattern</option> 63 <option value="pattern">Custom regex pattern</option>
66 </param> 64 </param>
67 <when value="beginning"> 65 <when value="beginning" />
68 <param name="pattern" type="hidden" value=">([^| ]+)" label="regex search pattern for ID" >
69 <sanitizer sanitize="False"/>
70 <validator type="regex" message="must include a group that returns an ID">^.*[(](?![?]:).*[)].*$</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