Mercurial > repos > iuc > ucsc_twobittofa
changeset 1:4a81db403bd9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa commit 8b84c1739e31ab884b81e214d72a65f030a5e950
| author | iuc |
|---|---|
| date | Wed, 13 Sep 2017 17:54:17 -0400 |
| parents | d025a40bbff1 |
| children | 356dc923f8d3 |
| files | twobittofa.xml |
| diffstat | 1 files changed, 30 insertions(+), 52 deletions(-) [+] |
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--- a/twobittofa.xml Fri Aug 19 06:30:41 2016 -0400 +++ b/twobittofa.xml Wed Sep 13 17:54:17 2017 -0400 @@ -1,85 +1,63 @@ <tool id="ucsc-twobittofa" name="twoBitToFa" version="@WRAPPER_VERSION@"> + <description>Convert all or part of .2bit file to FASTA</description> <macros> <token name="@WRAPPER_VERSION@">332</token> </macros> - - <description>Convert all or part of .2bit file to fasta</description> - <requirements> <requirement type="package" version="@WRAPPER_VERSION@">ucsc-twobittofa</requirement> </requirements> - <version_command><![CDATA[ echo "@WRAPPER_VERSION@" ]]></version_command> + <command><![CDATA[ +twoBitToFa +'$twobit_input' +'$fasta_output' - <command> -<![CDATA[ - twoBitToFa - '$twobit_input' - '$fasta_output' - - #if $seq - -seq='$seq' - #end if +#if $seq + -seq='$seq' +#end if - #if $start - -start=$start - #end if - - #if $end - -end=$end - #end if +#if str($start) + -start=$start +#end if - #if $seqList - -seqList='$seqList' - #end if +#if str($end) + -end=$end +#end if - $noMask -]]> - </command> +#if $seqList + -seqList='$seqList' +#end if + +$noMask + ]]></command> <inputs> - <param name="twobit_input" type="data" format="twobit" - label="Input TwoBit file" help=""/> - - <param argument="-seq" type="text" label="Restrict this to just one sequence - (Optional)" help="" optional="True"/> - - <param argument="-start" type="integer" label="Start at given position in - sequence (Optional)" help="Zero-based" optional="True"/> - - <param argument="-end" type="integer" label="End at given position in - sequence (Optional)" help="Non-inclusive" optional="True"/> - - <param argument="-seqList" type="data" format="txt" + <param name="twobit_input" type="data" format="twobit" label="Input TwoBit file" /> + <param argument="-seq" type="text" optional="true" label="Restrict this to just one sequence" help="Optional" /> + <param argument="-start" type="integer" optional="true" label="Start at given position in sequence" help="Zero-based, optional"/> + <param argument="-end" type="integer" optional="true" label="End at given position in sequence" help="Non-inclusive, optional" /> + <param argument="-seqList" type="data" format="txt" optional="true" label="File containing list of the desired sequence names (Optional)" help="It must be in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189 - where coordinates are half-open zero-based, i.e. [start,end)" - optional="True"/> - - <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue="" - checked="false" label="Convert sequence to all upper case?" help=""/> + where coordinates are half-open zero-based, i.e. [start,end)" /> + <param argument="-noMask" type="boolean" truevalue="-noMask" falsevalue="" checked="false" label="Convert sequence to all upper case?" /> </inputs> - <outputs> - <data format="fasta" name="fasta_output"/> + <data name="fasta_output" format="fasta" /> </outputs> - <tests> <test> <param name="twobit_input" value="input.2bit"/> <output name="fasta_output" file="output.fasta" /> </test> </tests> - <help><![CDATA[ **What it does** -twoBitToFa is a tool to convert all or part of .2bit file to fasta. +twoBitToFa is a tool to convert all or part of .2bit file to FASTA. -For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html/>`_. - +For more information, check the `user manual <https://genome.ucsc.edu/goldenpath/help/twoBit.html>`_. ]]></help> - <citations> </citations> </tool>