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comparison signature.xml @ 1:6218b518cd16 draft

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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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0:a2f293717ce3 1:6218b518cd16
1 <tool id="signature" name="Small RNA Signatures" version="2.0.5"> 1 <tool id="signature" name="Small RNA Signatures" version="2.1.0">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="1.1.2">bowtie</requirement>
5 <requirement type="package" version="0.7.7">pysam</requirement> 5 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
6 <requirement type="package" version="3.1.2">R</requirement> 6 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
7 <requirement type="package" version="2.14">biocbasics</requirement> 7 <!-- <requirement type="package" version="3.1.2">R</requirement> -->
8 <requirement type="package" version="1.9">numpy</requirement> 8 <requirement type="package" version="0.20_33=r3.2.2_0a">r-lattice</requirement>
9 </requirements> 9 </requirements>
10 <command interpreter="python"> 10 <command><![CDATA[
11 signature.py 11 python '$__tool_directory__'/signature.py
12 --input $refGenomeSource.input 12 --input '$refGenomeSource.input'
13 --inputFormat $refGenomeSource.input.ext 13 --inputFormat '$refGenomeSource.input.ext'
14 --minquery $minquery 14 --minquery $minquery
15 --maxquery $maxquery 15 --maxquery $maxquery
16 --mintarget $mintarget 16 --mintarget $mintarget
17 --maxtarget $maxtarget 17 --maxtarget $maxtarget
18 --minscope $minscope 18 --minscope $minscope
19 --maxscope $maxscope 19 --maxscope $maxscope
20 --outputOverlapDataframe $output 20 --outputOverlapDataframe $output
21 #if $refGenomeSource.genomeSource == "history": 21 #if $refGenomeSource.genomeSource == "history":
22 --referenceGenome $refGenomeSource.ownFile 22 --referenceGenome '$refGenomeSource.ownFile'
23 #else: 23 #else:
24 #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] 24 #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
25 --referenceGenome $reference 25 --referenceGenome '$reference'
26 --extract_index 26 --extract_index
27 #end if 27 #end if
28 --graph $graph_type 28 --graph $graph_type
29 --rcode $sigplotter 29 --rcode '$sigplotter'
30 </command> 30 ]]></command>
31 <inputs> 31 <inputs>
32 <conditional name="refGenomeSource"> 32 <conditional name="refGenomeSource">
33 <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"> 33 <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">
34 <option value="indexed">Use a built-in index</option> 34 <option value="indexed">Use a built-in index</option>
35 <option value="history">Use one from the history</option> 35 <option value="history">Use one from the history</option>