Mercurial > repos > drosofff > msp_sr_signature
diff signature.xml @ 1:6218b518cd16 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_signature commit 062e78aef14c4655d1b32d5f29ca543a50389b08
| author | drosofff |
|---|---|
| date | Wed, 07 Jun 2017 17:53:44 -0400 |
| parents | a2f293717ce3 |
| children | 229645380cb9 |
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--- a/signature.xml Wed Oct 21 11:35:25 2015 -0400 +++ b/signature.xml Wed Jun 07 17:53:44 2017 -0400 @@ -1,16 +1,16 @@ -<tool id="signature" name="Small RNA Signatures" version="2.0.5"> +<tool id="signature" name="Small RNA Signatures" version="2.1.0"> <description /> <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="0.7.7">pysam</requirement> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="2.14">biocbasics</requirement> - <requirement type="package" version="1.9">numpy</requirement> + <requirement type="package" version="1.1.2">bowtie</requirement> + <requirement type="package" version="1.11.2=py27_0">numpy</requirement> + <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> + <!-- <requirement type="package" version="3.1.2">R</requirement> --> + <requirement type="package" version="0.20_33=r3.2.2_0a">r-lattice</requirement> </requirements> - <command interpreter="python"> - signature.py - --input $refGenomeSource.input - --inputFormat $refGenomeSource.input.ext + <command><![CDATA[ + python '$__tool_directory__'/signature.py + --input '$refGenomeSource.input' + --inputFormat '$refGenomeSource.input.ext' --minquery $minquery --maxquery $maxquery --mintarget $mintarget @@ -19,15 +19,15 @@ --maxscope $maxscope --outputOverlapDataframe $output #if $refGenomeSource.genomeSource == "history": - --referenceGenome $refGenomeSource.ownFile + --referenceGenome '$refGenomeSource.ownFile' #else: #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] - --referenceGenome $reference + --referenceGenome '$reference' --extract_index #end if --graph $graph_type - --rcode $sigplotter - </command> + --rcode '$sigplotter' + ]]></command> <inputs> <conditional name="refGenomeSource"> <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">