Mercurial > repos > iuc > seqtk
diff seqtk_comp.xml @ 3:bc7d99f46a5d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
| author | iuc |
|---|---|
| date | Mon, 05 Jun 2017 13:27:11 -0400 |
| parents | f73729b62b51 |
| children | ecf1c30da3a2 |
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--- a/seqtk_comp.xml Fri Jan 01 14:49:42 2016 -0500 +++ b/seqtk_comp.xml Mon Jun 05 13:27:11 2017 -0400 @@ -1,33 +1,33 @@ <?xml version="1.0"?> <tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0"> - <description>get the nucleotide composition of FASTA/Q</description> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"/> - <expand macro="stdio"/> - <command><![CDATA[seqtk comp + <description>get the nucleotide composition of FASTA/Q</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ +seqtk comp #if $in_bed: --r $in_bed + -r '$in_bed' #end if - -$in_file | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1' - -> $default]]></command> - <inputs> - <expand macro="in_faq"/> - <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/> - </inputs> - <outputs> - <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/> - </outputs> - <tests> - <test> - <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/> - <output name="default" file="seqtk_comp.out" ftype="tabular"/> - </test> - </tests> - <help><![CDATA[ +'$in_file' | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1' +> '$default' + ]]></command> + <inputs> + <expand macro="in_faq"/> + <param name="in_bed" type="data" format="bed" optional="true" label="BED file"/> + </inputs> + <outputs> + <data name="default" format="tabular" label="Nucleotide composition of $in_file.name"/> + </outputs> + <tests> + <test> + <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/> + <output name="default" file="seqtk_comp.out" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ **What it does** Reports composition of fasta/fastq sequences. For an example sequence like @@ -46,8 +46,7 @@ test0 11 4 2 2 2 0 0 1 0 0 0 0 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0 - @ATTRIBUTION@ -]]></help> - <expand macro="citation" /> + ]]></help> + <expand macro="citation" /> </tool>