Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 14:a05b107fd0c4 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit d568170c53bf34da0560546d70038b1c53eb301b
author drosofff
date Mon, 26 Jun 2017 12:06:12 -0400
parents 99009e0a7a4a
children 44d61fa7fb75
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13:99009e0a7a4a 14:a05b107fd0c4
1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.2.2"> 1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
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><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__'/sRbowtie.py
9 --input '$input'
10 --input-format '$input.extension'
11 --method '$method'
12 --v-mismatches $v_mismatches
13 --output-format $output_format
14 --output '$output'
15 --index-from '$refGenomeSource.genomeSource'
16 ## the very source of the index (indexed or fasta file)
17 --index-source
18 #if $refGenomeSource.genomeSource == "history": 8 #if $refGenomeSource.genomeSource == "history":
19 '$refGenomeSource.ownFile' 9 bowtie-build -f '$refGenomeSource.ownFile' local_index &&
20 #else: 10 #else:
21 '$refGenomeSource.index.fields.path' 11 ln -s local_index '$refGenomeSource.index.fields.path' &&
22 #end if 12 #end if
23 --aligned '$aligned' 13 #if $input.extension == "fasta":
24 --unaligned '$unaligned' 14 #set format = "-f"
25 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie 15 #elif $input.extension == "fastq":
16 #set format = "-q"
17 #end if
18
19 ## set the method_prefix
20 #if $method == "RNA":
21 #set method_prefix = "-v %s -M 1 --best --strata --norc" % (str($v_mismatches))
22 #elif $method == "unique":
23 #set method_prefix = "-v %s -m 1" % (str($v_mismatches))
24 #elif $method == "multiple":
25 #set method_prefix = "-v %s -M 1 --best --strata" % (str($v_mismatches))
26 #elif $method == "k_option":
27 #set method_prefix = "-v %s -k 1 --best" % (str($v_mismatches))
28 #elif $method == "n_option":
29 #set method_prefix = "-n %s -M 1 --best" % (str($v_mismatches))
30 #elif $method == "a_option":
31 #set method_prefix = "-v %s -a --best" % (str($v_mismatches))
32 #end if
33
34 ## set the extra_output
35 #if $additional_fasta == "No":
36 #set extra_output = ""
37 #elif $additional_fasta == "al":
38 #set extra_output = " --un %s" % str(unaligned)
39 #else:
40 #set extra_output = " --al %s --un %s" % (str($aligned), str(unaligned))
41 #end if
42
43 #set $method_postfix = "$method_prefix" + "$extra_output"
44
45 ## run the bowtie alignement
46 #if $output_format == "tabular":
47 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --suppress 6,7,8 "local_index" $format $input > $output
48 #elif $output_format == "sam":
49 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input > $output
50 #elif $output_format == "bam":
51 bowtie -p \${GALAXY_SLOTS:-4} $method_prefix -S "local_index" $format $input |samtools view -bS - > $output
52 #end if
53
26 ]]></command> 54 ]]></command>
27 <inputs> 55 <inputs>
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" /> 56 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
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"> 57 <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">
30 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option> 58 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>