Mercurial > repos > iuc > obi_sort
diff obisort.xml @ 4:0d63988e23c3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 07:53:40 +0000 |
| parents | 25393415c6c9 |
| children | aaf7754dafd3 |
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--- a/obisort.xml Mon May 10 19:26:16 2021 +0000 +++ b/obisort.xml Wed Sep 01 07:53:40 2021 +0000 @@ -1,62 +1,63 @@ -<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@"> - <description>sorts sequence records according to the value of a given attribute</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - - <command><![CDATA[ - @GUNZIP_INPUT@ - obisort - --without-progress-bar - -k '$key' - ${reverse} - @INPUT_FORMAT@ - @OUT_FORMAT@ - input - @GZIP_OUTPUT@ - > '$output' - @GENERATE_GALAXY_JSON@ - ]]></command> - <inputs> - <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" /> - <param name="key" type="text" label="key"/> - <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" /> - <expand macro="input_format_options_macro"/> - <expand macro="out_format_macro"/> - </inputs> - <outputs> - <data format="auto" name="output"/> - </outputs> - <tests> - <test> - <param name="input" value="output_obiclean_advanced.fasta" /> - <param name="key" value="count"/> - <param name="reverse" value="False"/> - <param name="out_format" value="fasta"/> - <output name="output" file="output_obisort.fasta" ftype="fasta"/> - </test> - <test> - <param name="input" value="output_obiclean_advanced.fasta" /> - <param name="key" value="count"/> - <param name="reverse" value="True"/> - <param name="out_format" value="fastq"/> - <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/> - </test> - </tests> - <help><![CDATA[ - -.. class:: infomark - -**What it does** - -obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric. - -@OBITOOLS_LINK@ - - ]]> - - </help> - <expand macro="citation" /> -</tool> +<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@"> + <description>sorts sequence records according to the value of a given attribute</description> + <expand macro="bio_tools"/> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command><![CDATA[ + @GUNZIP_INPUT@ + obisort + --without-progress-bar + -k '$key' + ${reverse} + @INPUT_FORMAT@ + @OUT_FORMAT@ + input + @GZIP_OUTPUT@ + > '$output' + @GENERATE_GALAXY_JSON@ + ]]></command> + <inputs> + <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" /> + <param name="key" type="text" label="key"/> + <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" /> + <expand macro="input_format_options_macro"/> + <expand macro="out_format_macro"/> + </inputs> + <outputs> + <data format="auto" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="output_obiclean_advanced.fasta" /> + <param name="key" value="count"/> + <param name="reverse" value="False"/> + <param name="out_format" value="fasta"/> + <output name="output" file="output_obisort.fasta" ftype="fasta"/> + </test> + <test> + <param name="input" value="output_obiclean_advanced.fasta" /> + <param name="key" value="count"/> + <param name="reverse" value="True"/> + <param name="out_format" value="fastq"/> + <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric. + +@OBITOOLS_LINK@ + + ]]> + + </help> + <expand macro="citation" /> +</tool>