Mercurial > repos > jpetteng > ectyper1_0
annotate ectyper.xml @ 3:4df890ffed44 draft default tip
Added samtools requirement
| author | jpetteng |
|---|---|
| date | Thu, 11 Jan 2018 11:37:40 -0500 |
| parents | 338b07ddaa10 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ectyper" name="ectyper" version="0.1"> |
| 2 <requirements> | |
| 3 <requirement type="package" version="0.1">ectyper</requirement> | |
| 3 | 4 <requirement type="package" version="0.1.16">samtools</requirement> |
| 0 | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 #if $jobtype.select == "asm" | |
| 8 ln -s $jobtype.draft sample.fasta; | |
| 9 #else if $jobtype.select == "se" | |
| 10 ln -s $jobtype.fastq1 sample_1.fastq; | |
| 11 #else if $jobtype.select == "pe" | |
| 12 ln -s $jobtype.fastq1 sample_1.fastq; | |
| 13 ln -s $jobtype.fastq2 sample_2.fastq; | |
| 14 #end if | |
| 15 | |
| 16 $__tool_directory__/ectyper | |
| 17 #if $jobtype.select == "asm" | |
| 18 -i sample.fasta | |
| 19 #else if $jobtype.select == "se" | |
| 20 -i sample_1.fastq | |
| 21 #else if $jobtype.select == "pe" | |
|
2
338b07ddaa10
Changed to only use one fastq when paired is selected - otherwise need to make workflow to handle concatenation
jpetteng
parents:
0
diff
changeset
|
22 -i sample_1.fastq |
| 0 | 23 #end if |
| 24 -d $percent_identity | |
| 25 -l $percent_length | |
| 26 -o "./"; cat ./output/output.csv > results.csv; | |
| 27 | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 30 <conditional name="jobtype"> | |
| 31 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | |
| 32 <option value="asm">Genome Assembly</option> | |
| 33 <option value="se">Single-End Reads</option> | |
|
2
338b07ddaa10
Changed to only use one fastq when paired is selected - otherwise need to make workflow to handle concatenation
jpetteng
parents:
0
diff
changeset
|
34 <option value="pe">Paired-End Reads (only first fastq will be used)</option> |
| 0 | 35 </param> |
| 36 <when value="asm"> | |
| 37 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
| 38 </when> | |
| 39 <when value="se"> | |
| 40 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 41 </when> | |
| 42 <when value="pe"> | |
| 43 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 44 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> | |
| 45 </when> | |
| 46 </conditional> | |
| 47 | |
| 48 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" /> | |
| 49 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" /> | |
| 50 | |
| 51 </inputs> | |
| 52 <outputs> | |
| 53 <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/> | |
| 54 </outputs> | |
| 55 | |
| 56 <help><![CDATA[ | |
| 57 | |
| 58 **Usage: ectyper** | |
| 59 | |
| 60 **INPUT** | |
| 61 | |
| 62 A fasta assembly or single or paired end reads | |
| 63 | |
| 64 **PERCENTIDENTITY** | |
| 65 | |
| 66 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. | |
| 67 | |
| 68 **PERCENTLENGTH** | |
| 69 | |
| 70 Percentage of length wanted to use against the database. From 0 to 100, default is 50%. | |
| 71 | |
| 72 https://github.com/phac-nml/ecoli_serotyping | |
| 73 | |
| 74 ]]></help> | |
| 75 </tool> |