Galaxy | 1909 |

1. Map Reads tool metadata

Miscellaneous

Name: 1. Map Reads

Description: to index, or lookup cached alignment

Id: map_reads

Guid: toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/map_reads/1.0.1

Version: 1.0.1

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolrepo.galaxytrakr.org/repos/jpayne/snp_pipeline/map_reads/1.0.1 (this tool)

map_reads

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

bzip2

1.0.6

package

bowtie2

2.3.5

package

boto3

1.9.134

package

python

3.6.8

package

Additional information about this tool

Command:

export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
        #if $reads.reads_select == 'collection'
            #set forward=$reads.coll.forward
            #set reverse=$reads.coll.reverse
        #end if
        python ${__tool_directory__}/snp-cache.py snp_mapped_reads 
            "\$(md5sum  $reference
                        $forward
                        $reverse 
                        | cut -c -32 | md5sum | cut -c -32)"
            -c "
                cp $reference ./reference.fasta
                #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
                    && cp $forward ./forward.gz
                    #set $forward="./forward.gz"
                #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
                    && cp $forward ./forward.bz2
                    #set $forward="./forward.bz2"
                #end if
                #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
                    && cp $reverse ./reverse.gz
                    #set $reverse="./reverse.gz"
                #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
                    && cp $reverse ./reverse.bz2
                    #set $reverse="./reverse.bz2"
                #end if
                && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference
                && bowtie2 -q -x ./reference -1 $forward -2 $reverse  -p \${GALAXY_SLOTS:-4} --reorder -X 1000
                "
        #if $reads.reads_select == 'collection'
            -o ${align_from_collection}
        #else
            -o ${align_from_history}
        #end if
            -l $cache_log
        && cat $cache_log
        #if $source.source_select == 'curated'
        && cp $reference $ref_out
        #end if

Interpreter: None

Is multi-byte: False

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

attributes: name

reference/lambda_virus.fasta
samples/sample1/sample1_1.fastq
samples/sample1/sample1_2.fastq
name

Test-2

source|reference: reference/lambda_virus.fasta
reads|reads_select: collection
source|source_select: history
reads|coll: paired collection

attributes: name

reference/lambda_virus.fasta
samples/sample1/sample1_1.fastq
samples/sample1/sample1_2.fastq
name

Test-3

attributes: name

reference/lambda_virus.fasta
samples/sample1/sample1_1.fastq.gz
samples/sample1/sample1_2.fastq.gz
name