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comparison obisort.xml @ 3:e614dcabd870 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 19:34:04 +0000
parents 0de27b538106
children b6d9ea2fb41b
comparison
equal deleted inserted replaced
2:12b9e285ca1c 3:e614dcabd870
1 <tool id="obi_sort" name="obisort" version="@TOOL_VERSION@"> 1 <tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</description> 2 <description>sorts sequence records according to the value of a given attribute</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 8
9 <command> 9 <command><![CDATA[
10 10 @GUNZIP_INPUT@
11 <![CDATA[ 11 obisort
12 obisort 12 --without-progress-bar
13 -k '$key' 13 -k '$key'
14 ${reverse} 14 ${reverse}
15 '$input' > '$output' 15 @INPUT_FORMAT@
16 ]]> 16 @OUT_FORMAT@
17 17 input
18 </command> 18 @GZIP_OUTPUT@
19 19 > '$output'
20 @GENERATE_GALAXY_JSON@
21 ]]></command>
20 <inputs> 22 <inputs>
21 <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" /> 23 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" />
22 <param name="key" type="text" label="key" /> 24 <param name="key" type="text" label="key"/>
23 <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" /> 25 <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
24 <param name="out_format" type="select" label="Output data type"> 26 <expand macro="input_format_options_macro"/>
25 <option value="fasta">fasta</option> 27 <expand macro="out_format_macro"/>
26 <option value="fastq">fastq</option>
27 </param>
28
29 </inputs> 28 </inputs>
30 <outputs> 29 <outputs>
31 <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" > 30 <data format="auto" name="output"/>
32 <change_format>
33 <when input="out_format" value="fasta" format="fasta" />
34 </change_format>
35 </data>
36 </outputs> 31 </outputs>
37 <tests> 32 <tests>
38 <test> 33 <test>
39 <param name="input" value="output_obiclean_advanced.fasta" /> 34 <param name="input" value="output_obiclean_advanced.fasta" />
40 <param name="key" value="count"/> 35 <param name="key" value="count"/>
45 <test> 40 <test>
46 <param name="input" value="output_obiclean_advanced.fasta" /> 41 <param name="input" value="output_obiclean_advanced.fasta" />
47 <param name="key" value="count"/> 42 <param name="key" value="count"/>
48 <param name="reverse" value="True"/> 43 <param name="reverse" value="True"/>
49 <param name="out_format" value="fastq"/> 44 <param name="out_format" value="fastq"/>
50 <output name="output" file="output_obisort.fastq" ftype="fastq"/> 45 <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/>
51 </test> 46 </test>
52 </tests> 47 </tests>
53 <help><![CDATA[ 48 <help><![CDATA[
54 49
55 .. class:: infomark 50 .. class:: infomark