| Next changeset 1:dbcc6d233eed (2018-01-10) |
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Commit message:
Uploaded |
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added:
ectyper.xml |
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| diff -r 000000000000 -r 4724d20b14de ectyper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ectyper.xml Wed Jan 10 14:20:54 2018 -0500 |
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| @@ -0,0 +1,74 @@ +<tool id="ectyper" name="ectyper" version="0.1"> + <requirements> + <requirement type="package" version="0.1">ectyper</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $jobtype.select == "asm" + ln -s $jobtype.draft sample.fasta; + #else if $jobtype.select == "se" + ln -s $jobtype.fastq1 sample_1.fastq; + #else if $jobtype.select == "pe" + ln -s $jobtype.fastq1 sample_1.fastq; + ln -s $jobtype.fastq2 sample_2.fastq; + #end if + + $__tool_directory__/ectyper + #if $jobtype.select == "asm" + -i sample.fasta + #else if $jobtype.select == "se" + -i sample_1.fastq + #else if $jobtype.select == "pe" + -i sample_1.fastq sample_2.fastq + #end if + -d $percent_identity + -l $percent_length + -o "./"; cat ./output/output.csv > results.csv; + + ]]></command> + <inputs> + <conditional name="jobtype"> + <param name="select" type="select" label="Assembly or FASTQ Reads?"> + <option value="asm">Genome Assembly</option> + <option value="se">Single-End Reads</option> + <option value="pe">Paired-End Reads</option> + </param> + <when value="asm"> + <param name="draft" type="data" format="fasta" label="FASTA" /> + </when> + <when value="se"> + <param name="fastq1" type="data" format="fastq" label="FASTQ" /> + </when> + <when value="pe"> + <param name="fastq1" type="data" format="fastq" label="FASTQ" /> + <param name="fastq2" type="data" format="fastq" label="FASTQ" /> + </when> + </conditional> + + <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" /> + <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" /> + + </inputs> + <outputs> + <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/> + </outputs> + + <help><![CDATA[ + +**Usage: ectyper** + +**INPUT** + +A fasta assembly or single or paired end reads + +**PERCENTIDENTITY** + +Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. + +**PERCENTLENGTH** + +Percentage of length wanted to use against the database. From 0 to 100, default is 50%. + +https://github.com/phac-nml/ecoli_serotyping + + ]]></help> +</tool> |