Mercurial > repos > drosofff > mir_parser

comparison MirParser.xml @ 5:74394e39ad22 draft

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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
comparison
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4:933475df0fd2 5:74394e39ad22
1 <tool id="MirParser" name="Parse miRNAs" version="0.9.4"> 1 <tool id="MirParser" name="Parse miRNAs" version="0.9.6">
2 <description>from aligment files</description> 2 <description>from aligment files</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="1.9">numpy</requirement> 6 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
7 <requirement type="package" version="3.1.2">R</requirement> 7 <requirement type="package" version="0.20_33=r3.3.1_0">r-lattice</requirement>
8 <requirement type="package" version="2.14">biocbasics</requirement>
9 <requirement type="package" version="1.2">samtools</requirement>
10 </requirements> 8 </requirements>
11 <command interpreter="python"> 9 <command><![CDATA[
12 MirParser.py 10 python '$__tool_directory__'/MirParser.py
13 #if $refGenomeSource.genomeSource == "history": 11 #if $refGenomeSource.genomeSource == "history":
14 $refGenomeSource.ownFile ## index source sys.arg[1] 12 '$refGenomeSource.ownFile' ## index source sys.arg[1]
15 --do_not_extract_index ## sys.argv[2] 13 --do_not_extract_index ## sys.argv[2]
16 #else: 14 #else:
17 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] 15 #silent reference = filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
18 $reference ## sys.argv[1] 16 '$reference' ## sys.argv[1]
19 --extract_index ## sys.argv[2] 17 --extract_index ## sys.argv[2]
20 #end if 18 #end if
21 $output1 ## for pre-mirs ## sys.argv[3] 19 '$output1' ## for pre-mirs ## sys.argv[3]
22 $output2 ## for mature mirs ## sys.argv[4] 20 '$output2' ## for mature mirs ## sys.argv[4]
23 $GFF3 ## sys.argv[5] 21 '$GFF3' ## sys.argv[5]
24 #if $plotting.plottingOption == "yes": 22 #if $plotting.plottingOption == "yes":
25 $lattice_dataframe ## sys.argv[6] 23 '$lattice_dataframe' ## sys.argv[6]
26 $plotCode ## sys.argv[7] 24 '$plotCode' ## sys.argv[7]
27 $latticePDF ## sys.argv[8] 25 '$latticePDF' ## sys.argv[8]
28 #else: 26 #else:
29 "dummy_dataframe_path" ## sys.argv[6] 27 "dummy_dataframe_path" ## sys.argv[6]
30 "dummy_plotCode" ## sys.argv[7] 28 "dummy_plotCode" ## sys.argv[7]
31 "dummy_latticePDF" ## sys.argv[8] 29 "dummy_latticePDF" ## sys.argv[8]
32 #end if 30 #end if
33 #for $i in $refGenomeSource.input_list 31 #for $i in $refGenomeSource.input_list
34 $i $i.ext "$i.name" ## sys.argv[9,10,11] modulo 3 32 '$i' '$i.ext' "$i.name" ## sys.argv[9,10,11] modulo 3
35 #end for 33 #end for
36 #silent plottingoption = $plotting.plottingOption 34 #silent plottingoption = $plotting.plottingOption
37 </command> 35 ]]></command>
38 <inputs> 36 <inputs>
39 <conditional name="refGenomeSource"> 37 <conditional name="refGenomeSource">
40 <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"> 38 <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">
41 <option value="indexed">Use a built-in index</option> 39 <option value="indexed">Use a built-in index</option>
42 <option value="history">Use one from the history</option> 40 <option value="history">Use one from the history</option>