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

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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
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4:63b47deab5ff 5:16dc1dbb4cb2
1 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>Filters sequence file</description> 2 <description>Filters sequence file</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @GUNZIP_INPUT@ 10 @GUNZIP_INPUT@
11 11
37 @GZIP_OUTPUT@ 37 @GZIP_OUTPUT@
38 > '$output' 38 > '$output'
39 @GENERATE_GALAXY_JSON@ 39 @GENERATE_GALAXY_JSON@
40 ]]></command> 40 ]]></command>
41 <inputs> 41 <inputs>
42 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" /> 42 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file"/>
43 <conditional name="options_grep"> 43 <conditional name="options_grep">
44 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option" > 44 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option">
45 <option value="sequence" selected="true">sequence</option> 45 <option value="sequence" selected="true">sequence</option>
46 <option value="definition">definition</option> 46 <option value="definition">definition</option>
47 <option value="identifier">identifier</option> 47 <option value="identifier">identifier</option>
48 <option value="idlist">idlist</option> 48 <option value="idlist">idlist</option>
49 <option value="attribute">attribute</option> 49 <option value="attribute">attribute</option>
51 <option value="predicat">predicat</option> 51 <option value="predicat">predicat</option>
52 <option value="lmax">lmax</option> 52 <option value="lmax">lmax</option>
53 <option value="lmin">lmin</option> 53 <option value="lmin">lmin</option>
54 </param> 54 </param>
55 <when value="sequence"> 55 <when value="sequence">
56 <param name="sequence" type="text" label="Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive." > 56 <param name="sequence" type="text" label="Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive.">
57 <expand macro="sanitizer" /> 57 <expand macro="sanitizer"/>
58 </param> 58 </param>
59 </when> 59 </when>
60 <when value="definition"> 60 <when value="definition">
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." > 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.">
62 <expand macro="sanitizer" /> 62 <expand macro="sanitizer"/>
63 </param> 63 </param>
64 </when> 64 </when>
65 <when value="identifier"> 65 <when value="identifier">
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." > 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." >
67 <expand macro="sanitizer" /> 67 <expand macro="sanitizer"/>
68 </param> 68 </param>
69 </when> 69 </when>
70 <when value="idlist"> 70 <when value="idlist">
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." /> 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."/>
72 </when> 72 </when>
73 <when value="attribute"> 73 <when value="attribute">
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." > 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.">
75 <expand macro="sanitizer" /> 75 <expand macro="sanitizer"/>
76 </param> 76 </param>
77 </when> 77 </when>
78 <when value="hasattribute"> 78 <when value="hasattribute">
79 <param name="hasattribute" type="text" label="Selects sequence records having an attribute who is key." > 79 <param name="hasattribute" type="text" label="Selects sequence records having an attribute who is key.">
80 <expand macro="sanitizer" /> 80 <expand macro="sanitizer" />
81 </param> 81 </param>
82 </when> 82 </when>
83 <when value="predicat"> 83 <when value="predicat">
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." > 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.">
85 <expand macro="sanitizer" /> 85 <expand macro="sanitizer"/>
86 </param> 86 </param>
87 </when> 87 </when>
88 <when value="lmax"> 88 <when value="lmax">
89 <param name="lmax" type="text" label="lmax" help="Keeps sequence records whose sequence length is equal or shorter than lmax" /> 89 <param name="lmax" type="text" label="lmax" help="Keeps sequence records whose sequence length is equal or shorter than lmax"/>
90 </when> 90 </when>
91 <when value="lmin"> 91 <when value="lmin">
92 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/> 92 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/>
93 </when> 93 </when>
94 </conditional> 94 </conditional>
95 95 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)"/>
96 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)" />
97 <expand macro="input_format_options_macro"/> 96 <expand macro="input_format_options_macro"/>
98 <expand macro="out_format_macro"/> 97 <expand macro="out_format_macro"/>
99 </inputs> 98 </inputs>
100 <outputs> 99 <outputs>
101 <data format="auto" name="output"/> 100 <data format="auto" name="output"/>
102 </outputs> 101 </outputs>
103 <tests> 102 <tests>
104 <test> 103 <test expect_num_outputs="1">
105 <param name="input" value="illuminapairedend.output.fastq" /> 104 <!-- since the test data has large qualities it is sniffed as generic fastq which
106 <conditional name="options_grep"> 105 is not accepted py the parameter so the ftype is set, in this test we
107 <param name="options_grep_selector" value="lmin"/> 106 overwrite tis with the options_inputtype parameter and check if its set
108 <param name="lmin" value="80"/> 107 correctly on the CLI-->
109 </conditional> 108 <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsolexa"/>
110 <param name="v" value="true" /> 109 <conditional name="options_grep">
111 <param name="out_format" value="fastq" /> 110 <param name="options_grep_selector" value="lmin"/>
112 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/> 111 <param name="lmin" value="80"/>
113 </test> 112 </conditional>
114 <test> 113 <param name="v" value="true" />
115 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastq.gz" /> 114 <param name="options_inputtype" value="--sanger"/>
116 <conditional name="options_grep"> 115 <param name="out_format" value="fastq" />
117 <param name="options_grep_selector" value="predicat"/> 116 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/>
118 <param name="predicat" value='mode!="joined"'/> 117 <assert_command>
119 </conditional> 118 <has_text text="--sanger"/>
120 <param name="v" value="false" /> 119 </assert_command>
121 <param name="out_format" value="fasta" /> 120 </test>
122 <output name="output" file="output_obigrep_predicat.fasta.gz" ftype="fasta.gz" decompress="true"/> 121 <test expect_num_outputs="1">
122 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastqsolexa.gz"/>
123 <conditional name="options_grep">
124 <param name="options_grep_selector" value="predicat"/>
125 <param name="predicat" value='mode!="joined"'/>
126 </conditional>
127 <param name="v" value="false" />
128 <param name="out_format" value="fasta" />
129 <output name="output" file="output_obigrep_predicat.fasta.gz" ftype="fasta.gz" decompress="true"/>
130 <assert_command>
131 <has_text text="--solexa"/>
132 </assert_command>
123 </test> 133 </test>
124 </tests> 134 </tests>
125 <help><![CDATA[ 135 <help><![CDATA[
126 136
127 .. class:: infomark 137 .. class:: infomark