Mercurial > repos > estrain > serotypefinder
comparison serotypefinder.xml @ 0:1577ee103ed1 draft default tip
Uploaded
| author | estrain |
|---|---|
| date | Wed, 12 Jul 2023 17:09:33 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:1577ee103ed1 |
|---|---|
| 1 <tool id="serotypefinder" name="serotypefinder" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05"> | |
| 2 <requirements> | |
| 3 <requirement type="package">serotypefinder</requirement> | |
| 4 </requirements> | |
| 5 <command detect_errors="exit_code"><![CDATA[ | |
| 6 | |
| 7 #if $reads.reads_select == 'collection' | |
| 8 #set $name = $reads.coll.name.replace(' ', '_') | |
| 9 #set $forward = $reads.coll.forward | |
| 10 #set $reverse = $reads.coll.reverse | |
| 11 #set $infile = $name + "_1.fastq " + $name + "_2.fastq" | |
| 12 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz') | |
| 13 gunzip -c $reverse > reverse.fastq; | |
| 14 #set $reverse = './reverse.fastq' | |
| 15 gunzip -c $forward > forward.fastq; | |
| 16 #set $forward = './forward.fastq' | |
| 17 #end if | |
| 18 ln -s $forward ${name}_1.fastq; | |
| 19 ln -s $reverse ${name}_2.fastq; | |
| 20 #else | |
| 21 #set $name = $reads.assembly.name.replace(' ', '_') | |
| 22 #set $ga = $reads.assembly | |
| 23 #set $infile = $name + ".fasta" | |
| 24 ln -s $ga ${name}.fasta; | |
| 25 #end if | |
| 26 serotypefinder -x -i $infile | |
| 27 | |
| 28 ]]></command> | |
| 29 <inputs> | |
| 30 <conditional name="reads"> | |
| 31 <param name="reads_select" type="select" label="Genome assembly or paired-end collection"> | |
| 32 <option value="collection">Paired collection from your history</option> | |
| 33 <option value="genome">Genome Assembly</option> | |
| 34 </param> | |
| 35 <when value="collection"> | |
| 36 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" /> | |
| 37 </when> | |
| 38 <when value="genome"> | |
| 39 <param label="Genome assembly" name="assembly" type="data" format="fasta"/> | |
| 40 </when> | |
| 41 </conditional> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data name="results" format="tabular" from_work_dir="results_tab.tsv" /> | |
| 45 </outputs> | |
| 46 <help><![CDATA[ | |
| 47 Serotype predictions for E.coli. | |
| 48 ]]></help> | |
| 49 <citations> | |
| 50 <citation type="bibtex"> | |
| 51 @misc{fleming, | |
| 52 title={serotypefinder - Serotype Prediction for E. coli}, | |
| 53 journal={epub}, publisher={epub}, | |
| 54 author={Scheutz, Flemming}, | |
| 55 year={2023}, month={Max}, | |
| 56 url={https://bitbucket.org/genomicepidemiology/serotypefinder/src/master}}, | |
| 57 | |
| 58 </citation> | |
| 59 </citations> | |
| 60 </tool> | |
| 61 |