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comparison obigrep.xml @ 4:02bab5ff7c37 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:17:23 +0000
parents fe7ec8a3d35e
children
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3:fe7ec8a3d35e 4:02bab5ff7c37
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 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="stdio"/> 8 <expand macro="stdio"/>
8 <command><![CDATA[ 9 <command><![CDATA[
9 @GUNZIP_INPUT@ 10 @GUNZIP_INPUT@
10 11
36 @GZIP_OUTPUT@ 37 @GZIP_OUTPUT@
37 > '$output' 38 > '$output'
38 @GENERATE_GALAXY_JSON@ 39 @GENERATE_GALAXY_JSON@
39 ]]></command> 40 ]]></command>
40 <inputs> 41 <inputs>
41 <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"/>
42 <conditional name="options_grep"> 43 <conditional name="options_grep">
43 <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">
44 <option value="sequence" selected="true">sequence</option> 45 <option value="sequence" selected="true">sequence</option>
45 <option value="definition">definition</option> 46 <option value="definition">definition</option>
46 <option value="identifier">identifier</option> 47 <option value="identifier">identifier</option>
47 <option value="idlist">idlist</option> 48 <option value="idlist">idlist</option>
48 <option value="attribute">attribute</option> 49 <option value="attribute">attribute</option>
50 <option value="predicat">predicat</option> 51 <option value="predicat">predicat</option>
51 <option value="lmax">lmax</option> 52 <option value="lmax">lmax</option>
52 <option value="lmin">lmin</option> 53 <option value="lmin">lmin</option>
53 </param> 54 </param>
54 <when value="sequence"> 55 <when value="sequence">
55 <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.">
56 <expand macro="sanitizer" /> 57 <expand macro="sanitizer"/>
57 </param> 58 </param>
58 </when> 59 </when>
59 <when value="definition"> 60 <when value="definition">
60 <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.">
61 <expand macro="sanitizer" /> 62 <expand macro="sanitizer"/>
62 </param> 63 </param>
63 </when> 64 </when>
64 <when value="identifier"> 65 <when value="identifier">
65 <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." >
66 <expand macro="sanitizer" /> 67 <expand macro="sanitizer"/>
67 </param> 68 </param>
68 </when> 69 </when>
69 <when value="idlist"> 70 <when value="idlist">
70 <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."/>
71 </when> 72 </when>
72 <when value="attribute"> 73 <when value="attribute">
73 <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.">
74 <expand macro="sanitizer" /> 75 <expand macro="sanitizer"/>
75 </param> 76 </param>
76 </when> 77 </when>
77 <when value="hasattribute"> 78 <when value="hasattribute">
78 <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.">
79 <expand macro="sanitizer" /> 80 <expand macro="sanitizer" />
80 </param> 81 </param>
81 </when> 82 </when>
82 <when value="predicat"> 83 <when value="predicat">
83 <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.">
84 <expand macro="sanitizer" /> 85 <expand macro="sanitizer"/>
85 </param> 86 </param>
86 </when> 87 </when>
87 <when value="lmax"> 88 <when value="lmax">
88 <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"/>
89 </when> 90 </when>
90 <when value="lmin"> 91 <when value="lmin">
91 <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"/>
92 </when> 93 </when>
93 </conditional> 94 </conditional>
94 95 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)"/>
95 <param name="v" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Invert the sequence record selection (option -v)" />
96 <expand macro="input_format_options_macro"/> 96 <expand macro="input_format_options_macro"/>
97 <expand macro="out_format_macro"/> 97 <expand macro="out_format_macro"/>
98 </inputs> 98 </inputs>
99 <outputs> 99 <outputs>
100 <data format="auto" name="output"/> 100 <data format="auto" name="output"/>
101 </outputs> 101 </outputs>
102 <tests> 102 <tests>
103 <test> 103 <test expect_num_outputs="1">
104 <param name="input" value="illuminapairedend.output.fastq" /> 104 <!-- since the test data has large qualities it is sniffed as generic fastq which
105 <conditional name="options_grep"> 105 is not accepted py the parameter so the ftype is set, in this test we
106 <param name="options_grep_selector" value="lmin"/> 106 overwrite tis with the options_inputtype parameter and check if its set
107 <param name="lmin" value="80"/> 107 correctly on the CLI-->
108 </conditional> 108 <param name="input" value="illuminapairedend.output.fastq" ftype="fastqsolexa"/>
109 <param name="v" value="true" /> 109 <conditional name="options_grep">
110 <param name="out_format" value="fastq" /> 110 <param name="options_grep_selector" value="lmin"/>
111 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/> 111 <param name="lmin" value="80"/>
112 </test> 112 </conditional>
113 <test> 113 <param name="v" value="true" />
114 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastq.gz" /> 114 <param name="options_inputtype" value="--sanger"/>
115 <conditional name="options_grep"> 115 <param name="out_format" value="fastq" />
116 <param name="options_grep_selector" value="predicat"/> 116 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/>
117 <param name="predicat" value='mode!="joined"'/> 117 <assert_command>
118 </conditional> 118 <has_text text="--sanger"/>
119 <param name="v" value="false" /> 119 </assert_command>
120 <param name="out_format" value="fasta" /> 120 </test>
121 <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>
122 </test> 133 </test>
123 </tests> 134 </tests>
124 <help><![CDATA[ 135 <help><![CDATA[
125 136
126 .. class:: infomark 137 .. class:: infomark