Mercurial > repos > iuc > obi_grep

comparison obigrep.xml @ 3:fe7ec8a3d35e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author iuc
date Mon, 10 May 2021 19:33:38 +0000
parents 71cb8b117c05
children 02bab5ff7c37
comparison
equal deleted inserted replaced
2:e9e49cf06b42 3:fe7ec8a3d35e
1 <tool id="obi_grep" name="obigrep" version="@TOOL_VERSION@"> 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="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <command><![CDATA[
9 @GUNZIP_INPUT@
8 10
9 <command>
10
11 <![CDATA[
12 obigrep 11 obigrep
12 --without-progress-bar
13 ${v} 13 ${v}
14 #if str($options_grep.options_grep_selector) == 'sequence' 14 #if str($options_grep.options_grep_selector) == 'sequence'
15 -s ${options_grep.sequence} 15 -s ${options_grep.sequence}
16 #else if str($options_grep.options_grep_selector) == 'definition' 16 #else if str($options_grep.options_grep_selector) == 'definition'
17 -D ${options_grep.definition} 17 -D ${options_grep.definition}
18 #else if str($options_grep.options_grep_selector) == 'identifier' 18 #else if str($options_grep.options_grep_selector) == 'identifier'
19 -I ${options_grep.identifier} 19 -I ${options_grep.identifier}
20 #else if str($options_grep.options_grep_selector) == 'idlist' 20 #else if str($options_grep.options_grep_selector) == 'idlist'
21 --id-list '$options_grep.idlist} 21 --id-list '${options_grep.idlist}'
22 #else if str($options_grep.options_grep_selector) == 'attribute' 22 #else if str($options_grep.options_grep_selector) == 'attribute'
23 -a ${options_grep.attribute} 23 -a ${options_grep.attribute}
24 #else if str($options_grep.options_grep_selector) == 'hasattribute' 24 #else if str($options_grep.options_grep_selector) == 'hasattribute'
25 -A ${options_grep.attribute} 25 -A ${options_grep.attribute}
26 #else if str($options_grep.options_grep_selector) == 'predicat' 26 #else if str($options_grep.options_grep_selector) == 'predicat'
28 #else if str($options_grep.options_grep_selector) == 'lmax' 28 #else if str($options_grep.options_grep_selector) == 'lmax'
29 -L ${options_grep.lmax} 29 -L ${options_grep.lmax}
30 #else if str($options_grep.options_grep_selector) == 'lmin' 30 #else if str($options_grep.options_grep_selector) == 'lmin'
31 -l ${options_grep.lmin} 31 -l ${options_grep.lmin}
32 #end if 32 #end if
33 '$input' > '$output' 33 @INPUT_FORMAT@
34 ]]> 34 @OUT_FORMAT@
35 35 input
36 </command> 36 @GZIP_OUTPUT@
37 37 > '$output'
38 @GENERATE_GALAXY_JSON@
39 ]]></command>
38 <inputs> 40 <inputs>
39 <param name="input" type="data" format="fasta,fastq" label="Input sequences file" /> 41 <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
40 <conditional name="options_grep"> 42 <conditional name="options_grep">
41 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option" > 43 <param name="options_grep_selector" type="select" label="Choose the sequence record selection option" >
42 <option value="sequence" selected="true">sequence</option> 44 <option value="sequence" selected="true">sequence</option>
43 <option value="definition">definition</option> 45 <option value="definition">definition</option>
44 <option value="identifier">identifier</option> 46 <option value="identifier">identifier</option>
89 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/> 91 <param name="lmin" type="text" label="lmin" help="Keeps sequence records whose sequence length is equal or longer than lmin"/>
90 </when> 92 </when>
91 </conditional> 93 </conditional>
92 94
93 <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)" />
94 <param name="out_format" type="select" label="Output data type"> 96 <expand macro="input_format_options_macro"/>
95 <option value="fasta">fasta</option> 97 <expand macro="out_format_macro"/>
96 <option value="fastq">fastq</option>
97 </param>
98
99 </inputs> 98 </inputs>
100 <outputs> 99 <outputs>
101 <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" > 100 <data format="auto" name="output"/>
102 <change_format>
103 <when input="out_format" value="fasta" format="fasta" />
104 </change_format>
105 </data>
106 </outputs> 101 </outputs>
107 <tests> 102 <tests>
108 <test> 103 <test>
109 <param name="input" value="illuminapairedend.output.fastq" /> 104 <param name="input" value="illuminapairedend.output.fastq" />
110 <conditional name="options_grep"> 105 <conditional name="options_grep">
111 <param name="options_grep_selector" value="lmin"/> 106 <param name="options_grep_selector" value="lmin"/>
112 <param name="lmin" value="80"/> 107 <param name="lmin" value="80"/>
113 </conditional> 108 </conditional>
114 <param name="v" value="true" /> 109 <param name="v" value="true" />
115 <param name="out_format" value="fastq" /> 110 <param name="out_format" value="fastq" />
116 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastq"/> 111 <output name="output" file="output_obigrep_lmin.fastq" ftype="fastqsanger"/>
117 </test> 112 </test>
118 <test> 113 <test>
119 <param name="input" value="illuminapairedend.output.fastq" /> 114 <param name="input" value="illuminapairedend.output.fastq.gz" ftype="fastq.gz" />
120 <conditional name="options_grep"> 115 <conditional name="options_grep">
121 <param name="options_grep_selector" value="predicat"/> 116 <param name="options_grep_selector" value="predicat"/>
122 <param name="predicat" value='mode!="joined"'/> 117 <param name="predicat" value='mode!="joined"'/>
123 </conditional> 118 </conditional>
124 <param name="v" value="false" /> 119 <param name="v" value="false" />
125 <param name="out_format" value="fasta" /> 120 <param name="out_format" value="fasta" />
126 <output name="output" file="output_obigrep_predicat.fasta" ftype="fasta"/> 121 <output name="output" file="output_obigrep_predicat.fasta.gz" ftype="fasta.gz" decompress="true"/>
127 </test> 122 </test>
128 </tests> 123 </tests>
129 <help><![CDATA[ 124 <help><![CDATA[
130 125
131 .. class:: infomark 126 .. class:: infomark