Mercurial > repos > iuc > obi_annotate

annotate obigrep.xml.orig @ 4:d0f6ac976373 draft

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/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:49:38 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1 <<<<<<< HEAD
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
2 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@" profile="@PROFILE@">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
3 <description>Filters sequence file</description>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
4 <macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
5 <import>macros.xml</import>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
6 </macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
8 <expand macro="stdio"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
9 <command><![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
10 @GUNZIP_INPUT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
11
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
12 obigrep
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
13 --without-progress-bar
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
14 ${v}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
15 #if str($options_grep.options_grep_selector) == 'sequence'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
16 -s ${options_grep.sequence}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
17 #else if str($options_grep.options_grep_selector) == 'definition'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
18 -D ${options_grep.definition}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
19 #else if str($options_grep.options_grep_selector) == 'identifier'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
20 -I ${options_grep.identifier}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
21 #else if str($options_grep.options_grep_selector) == 'idlist'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
22 --id-list '${options_grep.idlist}'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
23 #else if str($options_grep.options_grep_selector) == 'attribute'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
24 -a ${options_grep.attribute}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
25 #else if str($options_grep.options_grep_selector) == 'hasattribute'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
26 -A ${options_grep.attribute}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
27 #else if str($options_grep.options_grep_selector) == 'predicat'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
28 -p ${options_grep.predicat}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
29 #else if str($options_grep.options_grep_selector) == 'lmax'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
30 -L ${options_grep.lmax}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
31 #else if str($options_grep.options_grep_selector) == 'lmin'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
32 -l ${options_grep.lmin}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
33 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
34 @INPUT_FORMAT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
35 @OUT_FORMAT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
36 input
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
37 @GZIP_OUTPUT@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
38 > '$output'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
39 @GENERATE_GALAXY_JSON@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
40 ]]></command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
41 <inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
42 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
43 <conditional name="options_grep">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
44 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option" >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
45 <option value="sequence" selected="true">sequence</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
46 <option value="definition">definition</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
47 <option value="identifier">identifier</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
48 <option value="idlist">idlist</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
49 <option value="attribute">attribute</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
50 <option value="hasattribute">hasattribute</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
51 <option value="predicat">predicat</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
52 <option value="lmax">lmax</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
53 <option value="lmin">lmin</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
54 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
55 <when value="sequence">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
56 <param name="sequence" type="text" label="Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
57 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
58 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
59 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
60 <when value="definition">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
62 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
63 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
64 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
65 <when value="identifier">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
67 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
68 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
69 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
70 <when value="idlist">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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." />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
72 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
73 <when value="attribute">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
75 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
76 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
77 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
78 <when value="hasattribute">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
79 <param name="hasattribute" type="text" label="Selects sequence records having an attribute who is key." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
80 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
81 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
82 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
83 <when value="predicat">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
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." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
85 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
86 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
87 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
88 <when value="lmax">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
89 <param name="lmax" type="text" label="lmax" help="Keeps sequence records whose sequence length is equal or shorter than lmax" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
90 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
91 <when value="lmin">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
92 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
93 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
94 </conditional>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
95
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
96 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
97 <expand macro="input_format_options_macro"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
98 <expand macro="out_format_macro"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
99 </inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
100 <outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
101 <data format="auto" name="output"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
102 </outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
103 <tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
104 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
105 <param name="input" value="illuminapairedend.output.fastq" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
106 <conditional name="options_grep">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
107 <param name="options_grep_selector" value="lmin"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
108 <param name="lmin" value="80"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
109 </conditional>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
110 <param name="v" value="true" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
111 <param name="out_format" value="fastq" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
112 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
113 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
114 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
115 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastq.gz" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
116 <conditional name="options_grep">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
117 <param name="options_grep_selector" value="predicat"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
118 <param name="predicat" value='mode!="joined"'/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
119 </conditional>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
120 <param name="v" value="false" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
121 <param name="out_format" value="fasta" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
122 <output name="output" file="output_obigrep_predicat.fasta.gz" ftype="fasta.gz" decompress="true"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
123 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
124 </tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
125 <help><![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
126
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
127 .. class:: infomark
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
128
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
129 **What it does**
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
130
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
131 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.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
132
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
133 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
134
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
135 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.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
136
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
137 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.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
138
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
139 Sequence record selection options :
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
140 * sequence : Regular expression pattern to be tested against the sequence itself. ex: GAATTC
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
141
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
142 * definition : Regular expression pattern to be tested against the definition of the sequence record. ex: [Cc]hloroplast
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
143
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
144 * identifier : Regular expression pattern to be tested against the identifier of the sequence record. ex: ^GH
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
145
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
146 * idlist : points to a text file containing the list of sequence record identifiers to be selected.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
147
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
148 * 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'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
149
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
150 * hasattribute : Selects sequence records having an attribute whose key = KEY.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
151
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
152 * 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"
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
153
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
154 * lmax : Keeps sequence records whose sequence length is equal or shorter than lmax. ex : 100
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
155
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
156 * lmin : Selects sequence records whose sequence length is equal or longer than lmin. ex : 100
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
157
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
158 @OBITOOLS_LINK@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
159
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
160 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
161
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
162 </help>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
163 <expand macro="citation" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
164
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
165 </tool>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
166 =======
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
167 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
168 <description>Filters sequence file</description>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
169 <expand macro="bio_tools"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
170 <macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
171 <import>macros.xml</import>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
172 </macros>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
173 <expand macro="requirements"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
174 <expand macro="stdio"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
175
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
176 <command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
177
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
178 <![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
179 obigrep
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
180 ${v}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
181 #if str($options_grep.options_grep_selector) == 'sequence'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
182 -s ${options_grep.sequence}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
183 #else if str($options_grep.options_grep_selector) == 'definition'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
184 -D ${options_grep.definition}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
185 #else if str($options_grep.options_grep_selector) == 'identifier'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
186 -I ${options_grep.identifier}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
187 #else if str($options_grep.options_grep_selector) == 'idlist'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
188 --id-list '$options_grep.idlist}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
189 #else if str($options_grep.options_grep_selector) == 'attribute'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
190 -a ${options_grep.attribute}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
191 #else if str($options_grep.options_grep_selector) == 'hasattribute'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
192 -A ${options_grep.attribute}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
193 #else if str($options_grep.options_grep_selector) == 'predicat'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
194 -p ${options_grep.predicat}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
195 #else if str($options_grep.options_grep_selector) == 'lmax'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
196 -L ${options_grep.lmax}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
197 #else if str($options_grep.options_grep_selector) == 'lmin'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
198 -l ${options_grep.lmin}
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
199 #end if
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
200 '$input' > '$output'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
201 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
202
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
203 </command>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
204
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
205 <inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
206 <param name="input" type="data" format="fasta,fastq" label="Input sequences file" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
207 <conditional name="options_grep">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
208 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option" >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
209 <option value="sequence" selected="true">sequence</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
210 <option value="definition">definition</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
211 <option value="identifier">identifier</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
212 <option value="idlist">idlist</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
213 <option value="attribute">attribute</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
214 <option value="hasattribute">hasattribute</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
215 <option value="predicat">predicat</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
216 <option value="lmax">lmax</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
217 <option value="lmin">lmin</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
218 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
219 <when value="sequence">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
220 <param name="sequence" type="text" label="Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
221 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
222 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
223 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
224 <when value="definition">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
225 <param name="definition" type="text" label="Regular expression pattern to be tested against the definition of the sequence record. The pattern is case sensitive." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
226 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
227 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
228 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
229 <when value="identifier">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
230 <param name="identifier" type="text" label="Regular expression pattern to be tested against the identifier of the sequence record. The pattern is case sensitive." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
231 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
232 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
233 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
234 <when value="idlist">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
235 <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." />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
236 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
237 <when value="attribute">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
238 <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." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
239 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
240 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
241 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
242 <when value="hasattribute">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
243 <param name="hasattribute" type="text" label="Selects sequence records having an attribute who is key." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
244 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
245 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
246 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
247 <when value="predicat">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
248 <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." >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
249 <expand macro="sanitizer" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
250 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
251 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
252 <when value="lmax">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
253 <param name="lmax" type="text" label="lmax" help="Keeps sequence records whose sequence length is equal or shorter than lmax" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
254 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
255 <when value="lmin">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
256 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
257 </when>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
258 </conditional>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
259
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
260 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
261 <param name="out_format" type="select" label="Output data type">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
262 <option value="fasta">fasta</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
263 <option value="fastq">fastq</option>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
264 </param>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
265
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
266 </inputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
267 <outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
268 <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" >
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
269 <change_format>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
270 <when input="out_format" value="fasta" format="fasta" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
271 </change_format>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
272 </data>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
273 </outputs>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
274 <tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
275 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
276 <param name="input" value="illuminapairedend.output.fastq" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
277 <conditional name="options_grep">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
278 <param name="options_grep_selector" value="lmin"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
279 <param name="lmin" value="80"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
280 </conditional>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
281 <param name="v" value="true" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
282 <param name="out_format" value="fastq" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
283 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastq"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
284 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
285 <test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
286 <param name="input" value="illuminapairedend.output.fastq" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
287 <conditional name="options_grep">
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
288 <param name="options_grep_selector" value="predicat"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
289 <param name="predicat" value='mode!="joined"'/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
290 </conditional>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
291 <param name="v" value="false" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
292 <param name="out_format" value="fasta" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
293 <output name="output" file="output_obigrep_predicat.fasta" ftype="fasta"/>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
294 </test>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
295 </tests>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
296 <help><![CDATA[
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
297
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
298 .. class:: infomark
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
299
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
300 **What it does**
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
301
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
302 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.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
303
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
304 A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
305
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
306 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.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
307
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
308 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.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
309
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
310 Sequence record selection options :
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
311 * sequence : Regular expression pattern to be tested against the sequence itself. ex: GAATTC
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
312
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
313 * definition : Regular expression pattern to be tested against the definition of the sequence record. ex: [Cc]hloroplast
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
314
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
315 * identifier : Regular expression pattern to be tested against the identifier of the sequence record. ex: ^GH
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
316
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
317 * idlist : points to a text file containing the list of sequence record identifiers to be selected.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
318
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
319 * 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'
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
320
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
321 * hasattribute : Selects sequence records having an attribute whose key = KEY.
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
322
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
323 * 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"
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
324
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
325 * lmax : Keeps sequence records whose sequence length is equal or shorter than lmax. ex : 100
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
326
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
327 * lmin : Selects sequence records whose sequence length is equal or longer than lmin. ex : 100
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
328
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
329 @OBITOOLS_LINK@
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
330
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
331 ]]>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
332
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
333 </help>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
334 <expand macro="citation" />
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
335
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
336 </tool>
d0f6ac976373 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
337 >>>>>>> 7abad681f (add tools up until P)