Mercurial > repos > jpetteng > ectyper
annotate ecoli_serotyping/ectyper.xml @ 27:c74c953c6b06 draft
Uploaded
| author | jpetteng |
|---|---|
| date | Sun, 07 Jan 2018 15:20:17 -0500 |
| parents | 54ae509ceeef |
| children | 41301e1f075a |
| 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> | |
| 4 <requirement type="package">biopython</requirement> | |
| 5 <requirement type="package">blast</requirement> | |
| 6 <requirement type="package">samtools</requirement> | |
| 7 <requirement type="package">bcftools</requirement> | |
| 8 <requirement type="package">bowtie</requirement> | |
| 9 <requirement type="package">spades</requirement> | |
| 10 <requirement type="package">seqtk</requirement> | |
| 12 | 11 <requirement type="package">pandas</requirement> |
| 14 | 12 <requirement type="package">mash</requirement> |
| 0 | 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 | |
| 11 | 23 |
| 22 | 24 python $__tool_directory__/ectyper/ectyper.py |
| 1 | 25 #if $jobtype.select == "asm" |
| 26 -m 4 | |
| 27 -i sample.fasta | |
| 28 #else if $jobtype.select == "se" | |
| 29 -m 3 | |
| 30 -i sample_1.fastq | |
| 31 #else if $jobtype.select == "pe" | |
| 32 -m 2 | |
| 33 -i sample_1.fastq sample_2.fastq | |
| 34 #end if | |
| 35 -b $maptype.select; | |
|
4
e07f3859a242
Updated xml file to require ectyper itself as it should be available via conda.
jpetteng
parents:
1
diff
changeset
|
36 cat ectyper_result*/ectyper_result.txt > results.txt; |
| 0 | 37 |
| 38 ]]></command> | |
| 39 <inputs> | |
| 1 | 40 <conditional name="jobtype"> |
| 41 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | |
| 42 <option value="asm">Genome Assembly</option> | |
| 43 <option value="se">Single-End Reads</option> | |
| 44 <option value="pe">Paired-End Reads</option> | |
| 0 | 45 </param> |
| 1 | 46 <when value="asm"> |
| 47 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
| 48 </when> | |
| 49 <when value="se"> | |
| 50 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 51 </when> | |
| 52 <when value="pe"> | |
| 53 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 54 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> | |
| 55 </when> | |
| 56 </conditional> | |
| 57 | |
| 58 <conditional name="maptype"> | |
| 59 <param name="select" type="select" label="Algorithms for BWA mapping?"> | |
| 60 <option value="sam">sam</option> | |
| 0 | 61 <option value="mem">mem</option> |
| 62 </param> | |
| 1 | 63 </conditional> |
| 0 | 64 |
| 65 | |
| 66 </inputs> | |
| 67 <outputs> | |
| 68 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/> | |
| 69 </outputs> | |
| 70 <tests> | |
| 71 <test> | |
| 72 <output name="results" file="results.txt"/> | |
| 73 </test> | |
| 74 </tests> | |
| 75 <help><![CDATA[ | |
| 76 | |
| 77 **Usage: ectyper** | |
| 78 | |
| 79 **INPUT** | |
| 80 | |
| 1 | 81 A fasta assembly |
| 0 | 82 |
| 83 **PERCENTIDENTITY** | |
| 84 | |
| 85 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. | |
| 86 | |
| 87 **PERCENTLENGTH** | |
| 88 | |
| 89 Percentage of length wanted to use against the database. From 0 to 100, default is 50%. | |
| 90 | |
| 91 **verify** | |
| 92 | |
| 93 Enable E. Coli. verification | |
| 94 | |
| 95 **species** | |
| 96 | |
| 97 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time. | |
| 98 | |
| 99 **OUTPUT** | |
| 100 Directory location of output files. | |
| 101 ]]></help> | |
| 102 </tool> |