Mercurial > repos > drosofff > msp_sr_bowtie_parser

comparison sRbowtieParser.xml @ 1:ca3845fb0b31 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 70312b58ba246c07e70cdbd0a097f274f1386d09
author drosofff
date Mon, 18 Apr 2016 10:09:08 -0400
parents b996480cd604
children
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0:b996480cd604 1:ca3845fb0b31
1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.1"> 1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement> 5 <requirement type="package" version="0.7.7">pysam</requirement>
7 <requirement type="package" version="1.9">numpy</requirement> 6 <requirement type="package" version="1.9">numpy</requirement>
8 <requirement type="package" version="0.14">scipy</requirement>
9 </requirements> 7 </requirements>
10 <command interpreter="python"> 8 <command>
11 sRbowtieParser.py 9 python $__tool_directory__/sRbowtieParser.py
12 #if $refGenomeSource.genomeSource == "history": 10 #if $refGenomeSource.genomeSource == "history":
13 --IndexSource $refGenomeSource.ownFile 11 --IndexSource $refGenomeSource.ownFile
14 --ExtractDirective fastaSource 12 --ExtractDirective fastaSource
15 #else: 13 #else:
16 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] 14 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
27 #for $i in $refGenomeSource.input_list 25 #for $i in $refGenomeSource.input_list
28 $i.ext 26 $i.ext
29 #end for 27 #end for
30 --alignmentLabel 28 --alignmentLabel
31 #for $i in $refGenomeSource.input_list 29 #for $i in $refGenomeSource.input_list
32 "$i.name" 30 "$i.element_identifier"
33 #end for 31 #end for
34 32
35 </command> 33 </command>
36 <inputs> 34 <inputs>
37 <conditional name="refGenomeSource"> 35 <conditional name="refGenomeSource">
38 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 36 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
39 <option value="indexed">Use a built-in index</option> 37 <option value="indexed">Use a built-in index</option>
40 <option value="history">Use one from the history</option> 38 <option value="history">Use one from the history</option>
41 </param> 39 </param>
42 <when value="indexed"> 40 <when value="indexed">
43 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"> 41 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true">
44 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/> 42 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
45 </param> 43 </param>
46 </when> 44 </when>
47 <when value="history"> 45 <when value="history">
48 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" /> 46 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
49 <param name="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/> 47 <param name="input_list" type="data" format="tabular,sam,bam" label="Select multiple alignments to parse" multiple="true"/>
50 </when> 48 </when>
51 </conditional> <!-- refGenomeSource --> 49 </conditional> <!-- refGenomeSource -->
52 <param name="polarity" type="select" label="how to count sense and antisense reads"> 50 <param name="polarity" type="select" label="how to count sense and antisense reads">
53 <option value="both">count both sense and antisense reads</option> 51 <option value="both">count both sense and antisense reads</option>
54 <option value="forward">count only sense reads</option> 52 <option value="forward">count only sense reads</option>