Mercurial > repos > jpetteng > ectyper
annotate ecoli_serotyping/ectyper.xml @ 28:41301e1f075a draft
Uploaded
| author | jpetteng |
|---|---|
| date | Tue, 09 Jan 2018 10:38:16 -0500 |
| parents | 54ae509ceeef |
| children | 5442b9d2e5d1 |
| 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> | |
| 28 | 4 <requirement type="package">ectyper</requirement> |
| 0 | 5 </requirements> |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 1 | 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 | |
| 11 | 15 |
| 28 | 16 python $__tool_directory__/bin/ectyper |
| 1 | 17 #if $jobtype.select == "asm" |
| 18 -m 4 | |
| 19 -i sample.fasta | |
| 20 #else if $jobtype.select == "se" | |
| 21 -m 3 | |
| 22 -i sample_1.fastq | |
| 23 #else if $jobtype.select == "pe" | |
| 24 -m 2 | |
| 25 -i sample_1.fastq sample_2.fastq | |
| 26 #end if | |
| 27 -b $maptype.select; | |
|
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e07f3859a242
Updated xml file to require ectyper itself as it should be available via conda.
jpetteng
parents:
1
diff
changeset
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28 cat ectyper_result*/ectyper_result.txt > results.txt; |
| 0 | 29 |
| 30 ]]></command> | |
| 31 <inputs> | |
| 1 | 32 <conditional name="jobtype"> |
| 33 <param name="select" type="select" label="Assembly or FASTQ Reads?"> | |
| 34 <option value="asm">Genome Assembly</option> | |
| 35 <option value="se">Single-End Reads</option> | |
| 36 <option value="pe">Paired-End Reads</option> | |
| 0 | 37 </param> |
| 1 | 38 <when value="asm"> |
| 39 <param name="draft" type="data" format="fasta" label="FASTA" /> | |
| 40 </when> | |
| 41 <when value="se"> | |
| 42 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 43 </when> | |
| 44 <when value="pe"> | |
| 45 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> | |
| 46 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> | |
| 47 </when> | |
| 48 </conditional> | |
| 49 | |
| 50 <conditional name="maptype"> | |
| 51 <param name="select" type="select" label="Algorithms for BWA mapping?"> | |
| 52 <option value="sam">sam</option> | |
| 0 | 53 <option value="mem">mem</option> |
| 54 </param> | |
| 1 | 55 </conditional> |
| 0 | 56 |
| 57 | |
| 58 </inputs> | |
| 59 <outputs> | |
| 60 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/> | |
| 61 </outputs> | |
| 62 <tests> | |
| 63 <test> | |
| 64 <output name="results" file="results.txt"/> | |
| 65 </test> | |
| 66 </tests> | |
| 67 <help><![CDATA[ | |
| 68 | |
| 69 **Usage: ectyper** | |
| 70 | |
| 71 **INPUT** | |
| 72 | |
| 1 | 73 A fasta assembly |
| 0 | 74 |
| 75 **PERCENTIDENTITY** | |
| 76 | |
| 77 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. | |
| 78 | |
| 79 **PERCENTLENGTH** | |
| 80 | |
| 81 Percentage of length wanted to use against the database. From 0 to 100, default is 50%. | |
| 82 | |
| 83 **verify** | |
| 84 | |
| 85 Enable E. Coli. verification | |
| 86 | |
| 87 **species** | |
| 88 | |
| 89 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time. | |
| 90 | |
| 91 **OUTPUT** | |
| 92 Directory location of output files. | |
| 93 ]]></help> | |
| 94 </tool> |