Mercurial > repos > iuc > mykrobe_predict

annotate macro.xml @ 0:33463c79e697 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
author iuc
date Sat, 13 Jan 2018 09:02:31 -0500
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33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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1 <?xml version="1.0"?>
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="0.5.6">mykrobe</requirement>
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6 </requirements>
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7 </xml>
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9 <token name="@select_inputs@">
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10 <![CDATA[
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11 #set $name='sample'
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12 #set $type='fastq'
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13 ## Adding sample name, indicate specie and inputs fastq(s) files
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14 #if $data_type.type == "paired":
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16 ln -s '$data_type.fastq_input1' sample_1.fastq &&
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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17 ln -s '$data_type.fastq_input2' sample_2.fastq &&
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20 #elif $data_type.type == "collection":
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21 #set $name=str($data_type.fastq_input1.name)
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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22 ln -s '$data_type.fastq_input1.forward' '$data_type.fastq_input1.name'_1.fastq &&
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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23 ln -s '$data_type.fastq_input1.reverse' '$data_type.fastq_input1.name'_2.fastq &&
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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25 #elif $data_type.type == "single":
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28 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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29 ln -s '$data_type.fastq_input1' sample.fastq &&
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31 #end if
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33 #if $data_type.fastq_input1.is_of_type('bam'):
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34 ln -s '$data_type.fastq_input1' sample.bam &&
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
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35 #set $type='bam'
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36 #end if
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38 #end if
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39 ]]>
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40 </token>
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42 <xml name="inputs">
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43 <conditional name="data_type">
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44 <param name="type" type="select" label="Specify the read type.">
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45 <option value="single">Single-end Data</option>
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46 <option value="paired">Paired-end Data</option>
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47 <option value="collection">Collection Paired-end Data</option>
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48 </param>
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49 <when value="single">
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50 <param name="fastq_input1" type="data" format="fastqsanger, fastq,fasta,bam" label="Single end read file(s)"/>
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51 </when>
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52 <when value="paired">
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53 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
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54 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
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55 </when>
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56 <when value="collection">
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57 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
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58 </when>
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59 </conditional>
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60 </xml>
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61
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62 <token name="@ATTRIBUTION@">
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63 <![CDATA[
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64
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65 **MyKrobe predict - Antibiotic resistance predictions**
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66
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67 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
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68 using Bruijn graph.
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69 ]]>
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70 </token>
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71
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72 <xml name="citation">
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73 <citations>
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74 <citation type="doi">10.1038/ncomms10063</citation>
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75 </citations>
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76 </xml>
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77 </macros>