Mercurial > repos > jpetteng > ectyper
annotate ecoli_serotyping/ectyper.xml @ 10:5b52b3842765 draft
Uploaded
| author | jpetteng |
|---|---|
| date | Sat, 06 Jan 2018 13:32:23 -0500 |
| parents | 148199949636 |
| children | 8cb863e320e7 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ectyper" name="ectyper" version="2.0"> |
| 2 <requirements> | |
| 3 <requirement type="package" version="3.6.3">python</requirement> | |
| 10 | 4 <requirement type="package">ectyper</requirement> |
| 0 | 5 <requirement type="package">biopython</requirement> |
| 6 <requirement type="package">blast</requirement> | |
| 7 <requirement type="package">samtools</requirement> | |
| 8 <requirement type="package">bcftools</requirement> | |
| 9 <requirement type="package">bowtie</requirement> | |
| 10 <requirement type="package">spades</requirement> | |
| 11 <requirement type="package">seqtk</requirement> | |
| 12 # <requirement type="package">mash</requirement> | |
| 13 </requirements> | |
| 14 <command detect_errors="exit_code"><![CDATA[ | |
| 1 | 15 #if $jobtype.select == "asm" |
| 16 ln -s $jobtype.draft sample.fasta; | |
| 17 #else if $jobtype.select == "se" | |
| 18 ln -s $jobtype.fastq1 sample_1.fastq; | |
| 19 #else if $jobtype.select == "pe" | |
| 20 ln -s $jobtype.fastq1 sample_1.fastq; | |
| 21 ln -s $jobtype.fastq2 sample_2.fastq; | |
| 22 #end if | |
| 10 | 23 ectyper.py |
| 1 | 24 #if $jobtype.select == "asm" |
| 25 -m 4 | |
| 26 -i sample.fasta | |
| 27 #else if $jobtype.select == "se" | |
| 28 -m 3 | |
| 29 -i sample_1.fastq | |
| 30 #else if $jobtype.select == "pe" | |
| 31 -m 2 | |
| 32 -i sample_1.fastq sample_2.fastq | |
| 33 #end if | |
| 34 -b $maptype.select; | |
|
4
e07f3859a242
Updated xml file to require ectyper itself as it should be available via conda.
jpetteng
parents:
1
diff
changeset
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35 cat ectyper_result*/ectyper_result.txt > results.txt; |
| 0 | 36 |
| 37 ]]></command> | |
| 38 <inputs> | |
| 1 | 39 <conditional name="jobtype"> |
| 40 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | |
| 41 <option value="asm">Genome Assembly</option> | |
| 42 <option value="se">Single-End Reads</option> | |
| 43 <option value="pe">Paired-End Reads</option> | |
| 0 | 44 </param> |
| 1 | 45 <when value="asm"> |
| 46 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
| 47 </when> | |
| 48 <when value="se"> | |
| 49 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 50 </when> | |
| 51 <when value="pe"> | |
| 52 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 53 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> | |
| 54 </when> | |
| 55 </conditional> | |
| 56 | |
| 57 <conditional name="maptype"> | |
| 58 <param name="select" type="select" label="Algorithms for BWA mapping?"> | |
| 59 <option value="sam">sam</option> | |
| 0 | 60 <option value="mem">mem</option> |
| 61 </param> | |
| 1 | 62 </conditional> |
| 0 | 63 |
| 64 | |
| 65 </inputs> | |
| 66 <outputs> | |
| 67 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/> | |
| 68 </outputs> | |
| 69 <tests> | |
| 70 <test> | |
| 71 <output name="results" file="results.txt"/> | |
| 72 </test> | |
| 73 </tests> | |
| 74 <help><![CDATA[ | |
| 75 | |
| 76 **Usage: ectyper** | |
| 77 | |
| 78 **INPUT** | |
| 79 | |
| 1 | 80 A fasta assembly |
| 0 | 81 |
| 82 **PERCENTIDENTITY** | |
| 83 | |
| 84 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. | |
| 85 | |
| 86 **PERCENTLENGTH** | |
| 87 | |
| 88 Percentage of length wanted to use against the database. From 0 to 100, default is 50%. | |
| 89 | |
| 90 **verify** | |
| 91 | |
| 92 Enable E. Coli. verification | |
| 93 | |
| 94 **species** | |
| 95 | |
| 96 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time. | |
| 97 | |
| 98 **OUTPUT** | |
| 99 Directory location of output files. | |
| 100 ]]></help> | |
| 101 </tool> |