Mercurial > repos > drosofff > mir_parser
diff MirParser.xml @ 5:74394e39ad22 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
| author | drosofff |
|---|---|
| date | Sun, 11 Jun 2017 05:56:29 -0400 |
| parents | 933475df0fd2 |
| children |
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--- a/MirParser.xml Wed Oct 21 11:25:01 2015 -0400 +++ b/MirParser.xml Sun Jun 11 05:56:29 2017 -0400 @@ -1,40 +1,38 @@ -<tool id="MirParser" name="Parse miRNAs" version="0.9.4"> +<tool id="MirParser" name="Parse miRNAs" version="0.9.6"> <description>from aligment files</description> <requirements> - <requirement type="package" version="0.12.7">bowtie</requirement> - <requirement type="package" version="0.7.7">pysam</requirement> - <requirement type="package" version="1.9">numpy</requirement> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="package" version="2.14">biocbasics</requirement> - <requirement type="package" version="1.2">samtools</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="0.20_33=r3.3.1_0">r-lattice</requirement> </requirements> - <command interpreter="python"> - MirParser.py - #if $refGenomeSource.genomeSource == "history": - $refGenomeSource.ownFile ## index source sys.arg[1] - --do_not_extract_index ## sys.argv[2] - #else: - #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] - $reference ## sys.argv[1] + <command><![CDATA[ + python '$__tool_directory__'/MirParser.py + #if $refGenomeSource.genomeSource == "history": + '$refGenomeSource.ownFile' ## index source sys.arg[1] + --do_not_extract_index ## sys.argv[2] + #else: + #silent reference = filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] + '$reference' ## sys.argv[1] --extract_index ## sys.argv[2] - #end if - $output1 ## for pre-mirs ## sys.argv[3] - $output2 ## for mature mirs ## sys.argv[4] - $GFF3 ## sys.argv[5] - #if $plotting.plottingOption == "yes": - $lattice_dataframe ## sys.argv[6] - $plotCode ## sys.argv[7] - $latticePDF ## sys.argv[8] - #else: + #end if + '$output1' ## for pre-mirs ## sys.argv[3] + '$output2' ## for mature mirs ## sys.argv[4] + '$GFF3' ## sys.argv[5] + #if $plotting.plottingOption == "yes": + '$lattice_dataframe' ## sys.argv[6] + '$plotCode' ## sys.argv[7] + '$latticePDF' ## sys.argv[8] + #else: "dummy_dataframe_path" ## sys.argv[6] - "dummy_plotCode" ## sys.argv[7] + "dummy_plotCode" ## sys.argv[7] "dummy_latticePDF" ## sys.argv[8] - #end if - #for $i in $refGenomeSource.input_list - $i $i.ext "$i.name" ## sys.argv[9,10,11] modulo 3 - #end for - #silent plottingoption = $plotting.plottingOption -</command> + #end if + #for $i in $refGenomeSource.input_list + '$i' '$i.ext' "$i.name" ## sys.argv[9,10,11] modulo 3 + #end for + #silent plottingoption = $plotting.plottingOption + ]]></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">