Mercurial > repos > iuc > obi_sort
diff obisort.xml @ 3:e614dcabd870 draft
"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 |
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--- a/obisort.xml Thu Nov 28 15:51:52 2019 -0500 +++ b/obisort.xml Mon May 10 19:34:04 2021 +0000 @@ -1,67 +1,62 @@ -<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@"> - <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - - <command> - - <![CDATA[ - obisort - -k '$key' - ${reverse} - '$input' > '$output' - ]]> - - </command> - - <inputs> - <param name="input" type="data" format="fastq,fasta,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?" /> - <param name="out_format" type="select" label="Output data type"> - <option value="fasta">fasta</option> - <option value="fastq">fastq</option> - </param> - - </inputs> - <outputs> - <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" > - <change_format> - <when input="out_format" value="fasta" format="fasta" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input" value="output_obiclean_advanced.fasta" /> - <param name="key" value="count"/> - <param name="reverse" value="False"/> - <param name="out_format" value="fasta"/> - <output name="output" file="output_obisort.fasta" ftype="fasta"/> - </test> - <test> - <param name="input" value="output_obiclean_advanced.fasta" /> - <param name="key" value="count"/> - <param name="reverse" value="True"/> - <param name="out_format" value="fastq"/> - <output name="output" file="output_obisort.fastq" ftype="fastq"/> - </test> - </tests> - <help><![CDATA[ - -.. class:: infomark - -**What it does** - -obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric. - -@OBITOOLS_LINK@ - - ]]> - - </help> - <expand macro="citation" /> -</tool> +<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@"> + <description>sorts sequence records according to the value of a given attribute</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command><![CDATA[ + @GUNZIP_INPUT@ + obisort + --without-progress-bar + -k '$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>