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comparison obiconvert.xml @ 5:c5a81ce6414c 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 16:02:11 +0000
parents c62e77c0a83c
children
comparison
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4:c62e77c0a83c 5:c5a81ce6414c
1 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>converts sequence files to different output formats</description> 2 <description>converts sequence files to different output formats</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
27 @GZIP_OUTPUT@ 27 @GZIP_OUTPUT@
28 > '${output}' 28 > '${output}'
29 @GENERATE_GALAXY_JSON@ 29 @GENERATE_GALAXY_JSON@
30 ]]></command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" /> 32 <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)"/>
33 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" /> 33 <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database"/>
34 <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/> 34 <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
35 <expand macro="input_format_options_macro"/> 35 <expand macro="input_format_options_macro"/>
36 <expand macro="out_format_macro"/> 36 <expand macro="out_format_macro"/>
37 <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file" /> 37 <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file"/>
38 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" /> 38 <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?"/>
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb"> 41 <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
42 <filter>ecopcrdb == True</filter> 42 <filter>ecopcrdb == True</filter>
43 </data> 43 </data>
44 <data format="auto" name="output"/> 44 <data format="auto" name="output"/>
45 </outputs> 45 </outputs>
46 <tests> 46 <tests>
47 <test> 47 <test expect_num_outputs="1">
48 <param name="input" value="output_obisort.fasta" /> 48 <param name="input" value="output_obisort.fasta" />
49 <param name="options_inputtype" value="--fasta"/> 49 <param name="options_inputtype" value="--fasta"/>
50 <param name="options_seqtype" value="--nuc"/> 50 <param name="options_seqtype" value="--nuc"/>
51 <param name="out_format" value="fasta"/> 51 <param name="out_format" value="fasta"/>
52 <param name="ecopcrdb" value="false"/> 52 <param name="ecopcrdb" value="false"/>