Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 4:615d2550977f draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit b6de14061c479f0418cd89e26d6f5ac26e565a07
author drosofff
date Wed, 09 Nov 2016 11:20:44 -0500
parents 68b71bd388eb
children b2c1ffe6579a
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3:68b71bd388eb 4:615d2550977f
2 <description>for FASTA small reads</description> 2 <description>for FASTA small reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">bowtie</requirement> 4 <requirement type="package" version="1.1.2">bowtie</requirement>
5 <requirement type="package" version="1.2">samtools</requirement> 5 <requirement type="package" version="1.2">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> sRbowtie.py --input $input 7 <command><![CDATA[
8 --input-format $input.extension 8 python '$__tool_directory__'/sRbowtie.py
9 --method $method 9 --input '$input'
10 --v-mismatches $v_mismatches 10 --input-format '$input.extension'
11 --output-format $output_format 11 --method '$method'
12 --output $output 12 --v-mismatches $v_mismatches
13 --index-from $refGenomeSource.genomeSource 13 --output-format $output_format
14 ## the very source of the index (indexed or fasta file) 14 --output '$output'
15 --index-source 15 --index-from '$refGenomeSource.genomeSource'
16 #if $refGenomeSource.genomeSource == "history": 16 ## the very source of the index (indexed or fasta file)
17 $refGenomeSource.ownFile 17 --index-source
18 #else: 18 #if $refGenomeSource.genomeSource == "history":
19 $refGenomeSource.index.fields.path 19 '$refGenomeSource.ownFile'
20 #end if 20 #else:
21 --aligned $aligned 21 '$refGenomeSource.index.fields.path'
22 --unaligned $unaligned 22 #end if
23 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie 23 --aligned '$aligned'
24 </command> 24 --unaligned '$unaligned'
25 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
26 ]]></command>
25 <inputs> 27 <inputs>
26 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" /> 28 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
27 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select"> 29 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
28 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option> 30 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
29 <option value="unique">Match unique mappers on DNA reference index</option> 31 <option value="unique">Match unique mappers on DNA reference index</option>