Mercurial > repos > iuc > obi_grep

annotate obigrep.xml @ 5:16dc1dbb4cb2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
author iuc
date Thu, 30 Oct 2025 16:01:34 +0000
parents 63b47deab5ff
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
1 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@" profile="@PROFILE@">
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
2 <description>Filters sequence file</description>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
3 <macros>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
4 <import>macros.xml</import>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
5 </macros>
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
6 <expand macro="bio_tools"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
7 <expand macro="requirements"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
8 <expand macro="stdio"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
9 <command><![CDATA[
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
10 @GUNZIP_INPUT@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
11
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
12 obigrep
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
13 --without-progress-bar
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
14 ${v}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
15 #if str($options_grep.options_grep_selector) == 'sequence'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
16 -s ${options_grep.sequence}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
17 #else if str($options_grep.options_grep_selector) == 'definition'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
18 -D ${options_grep.definition}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
19 #else if str($options_grep.options_grep_selector) == 'identifier'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
20 -I ${options_grep.identifier}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
21 #else if str($options_grep.options_grep_selector) == 'idlist'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
22 --id-list '${options_grep.idlist}'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
23 #else if str($options_grep.options_grep_selector) == 'attribute'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
24 -a ${options_grep.attribute}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
25 #else if str($options_grep.options_grep_selector) == 'hasattribute'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
26 -A ${options_grep.attribute}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
27 #else if str($options_grep.options_grep_selector) == 'predicat'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
28 -p ${options_grep.predicat}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
29 #else if str($options_grep.options_grep_selector) == 'lmax'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
30 -L ${options_grep.lmax}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
31 #else if str($options_grep.options_grep_selector) == 'lmin'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
32 -l ${options_grep.lmin}
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
33 #end if
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
34 @INPUT_FORMAT@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
35 @OUT_FORMAT@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
36 input
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
37 @GZIP_OUTPUT@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
38 > '$output'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
39 @GENERATE_GALAXY_JSON@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
40 ]]></command>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
41 <inputs>
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
42 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
43 <conditional name="options_grep">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
44 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option">
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
45 <option value="sequence" selected="true">sequence</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
46 <option value="definition">definition</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
47 <option value="identifier">identifier</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
48 <option value="idlist">idlist</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
49 <option value="attribute">attribute</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
50 <option value="hasattribute">hasattribute</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
51 <option value="predicat">predicat</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
52 <option value="lmax">lmax</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
53 <option value="lmin">lmin</option>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
54 </param>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
55 <when value="sequence">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
56 <param name="sequence" type="text" label="Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive.">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
57 <expand macro="sanitizer"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
58 </param>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
59 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
60 <when value="definition">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
61 <param name="definition" type="text" label="Regular expression pattern to be tested against the definition of the sequence record. The pattern is case sensitive.">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
62 <expand macro="sanitizer"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
63 </param>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
64 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
65 <when value="identifier">
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
66 <param name="identifier" type="text" label="Regular expression pattern to be tested against the identifier of the sequence record. The pattern is case sensitive." >
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
67 <expand macro="sanitizer"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
68 </param>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
69 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
70 <when value="idlist">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
71 <param name="idlist" type="data" format="txt,tabular" label="points to a text file containing the list of sequence record identifiers to be selected. The file format consists in a single identifier per line."/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
72 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
73 <when value="attribute">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
74 <param name="attribute" type="text" label="Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. The pattern is case sensitive.">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
75 <expand macro="sanitizer"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
76 </param>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
77 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
78 <when value="hasattribute">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
79 <param name="hasattribute" type="text" label="Selects sequence records having an attribute who is key.">
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
80 <expand macro="sanitizer" />
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
81 </param>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
82 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
83 <when value="predicat">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
84 <param name="predicat" type="text" label="Python boolean expression to be evaluated for each sequence record." help="The attribute keys defined for each sequence record can be used in the expression as variable names. An extra variable named sequenceefers to the sequence record itself.">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
85 <expand macro="sanitizer"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
86 </param>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
87 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
88 <when value="lmax">
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
89 <param name="lmax" type="text" label="lmax" help="Keeps sequence records whose sequence length is equal or shorter than lmax"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
90 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
91 <when value="lmin">
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
92 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
93 </when>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
94 </conditional>
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
95 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)"/>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
96 <expand macro="input_format_options_macro"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
97 <expand macro="out_format_macro"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
98 </inputs>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
99 <outputs>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
100 <data format="auto" name="output"/>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
101 </outputs>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
102 <tests>
5
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
103 <test expect_num_outputs="1">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
104 <!-- since the test data has large qualities it is sniffed as generic fastq which
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
105 is not accepted py the parameter so the ftype is set, in this test we
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
106 overwrite tis with the options_inputtype parameter and check if its set
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
107 correctly on the CLI-->
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
108 <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsolexa"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
109 <conditional name="options_grep">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
110 <param name="options_grep_selector" value="lmin"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
111 <param name="lmin" value="80"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
112 </conditional>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
113 <param name="v" value="true" />
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
114 <param name="options_inputtype" value="--sanger"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
115 <param name="out_format" value="fastq" />
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
116 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
117 <assert_command>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
118 <has_text text="--sanger"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
119 </assert_command>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
120 </test>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
121 <test expect_num_outputs="1">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
122 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsolexa.gz"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
123 <conditional name="options_grep">
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
124 <param name="options_grep_selector" value="predicat"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
125 <param name="predicat" value='mode!="joined"'/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
126 </conditional>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
127 <param name="v" value="false" />
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
128 <param name="out_format" value="fasta" />
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
129 <output name="output" file="output_obigrep_predicat.fasta.gz" ftype="fasta.gz" decompress="true"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
130 <assert_command>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
131 <has_text text="--solexa"/>
16dc1dbb4cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit a01e3c562cf5d62af522b893a25abde6476a1f45
iuc
parents: 4
diff changeset
132 </assert_command>
4
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
133 </test>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
134 </tests>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
135 <help><![CDATA[
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
136
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
137 .. class:: infomark
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
138
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
139 **What it does**
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
140
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
141 The obigrep command is in some way analog to the standard Unix grep command. It selects a subset of sequence records from a sequence file.
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
142
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
143 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
144
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
145 Instead of working text line by text line as the standard Unix tool, selection is done sequence record by sequence record. A large set of options allows refining selection on any of the sequence record elements.
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
146
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
147 Moreover obigrep allows specifying simultaneously several conditions (that take the value TRUE or FALSE) and only the sequence records that fulfill all the conditions (all conditions are TRUE) are selected.
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
148
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
149 Sequence record selection options :
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
150 * sequence : Regular expression pattern to be tested against the sequence itself. ex: GAATTC
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
151
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
152 * definition : Regular expression pattern to be tested against the definition of the sequence record. ex: [Cc]hloroplast
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
153
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
154 * identifier : Regular expression pattern to be tested against the identifier of the sequence record. ex: ^GH
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
155
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
156 * idlist : points to a text file containing the list of sequence record identifiers to be selected.
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
157
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
158 * attribute : Regular expression pattern matched against the attributes of the sequence record. the value of this attribute is of the form : key:regular_pattern. ex:'family_name:Asteraceae'
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
159
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
160 * hasattribute : Selects sequence records having an attribute whose key = KEY.
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
161
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
162 * predicat : Python boolean expression to be evaluated for each sequence record. The attribute keys defined for each sequence record can be used in the expression as variable names. An extra variable named ‘sequence’ refers to the sequence record itself. ex: mode!="joined"
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
163
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
164 * lmax : Keeps sequence records whose sequence length is equal or shorter than lmax. ex : 100
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
165
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
166 * lmin : Selects sequence records whose sequence length is equal or longer than lmin. ex : 100
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
167
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
168 @OBITOOLS_LINK@
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
169
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
170 ]]>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
171
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
172 </help>
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
173 <expand macro="citation" />
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
174
63b47deab5ff "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 3
diff changeset
175 </tool>