Mercurial > repos > cstrittmatter > ectyper_v1

annotate ectyper.xml @ 0:4b7f728bcd11 draft

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author cstrittmatter
date Wed, 28 Mar 2018 14:05:50 -0400
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children 5bf7e686149f
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1 <tool id="ectyper" name="ectyper" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="0.1">ectyper</requirement>
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4 <requirement type="package" version="3.5">python</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #if $jobtype.select == "asm"
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8 ln -s $jobtype.draft ${draft.name}.fasta;
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9 #else if $jobtype.select == "se"
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10 ln -s $jobtype.fastq1 ${fastq1.name}_1.fastq;
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11 #else if $jobtype.select == "pe"
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12 ln -s $jobtype.fastq1 ${fastq1.name}.fastq;
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13 ln -s $jobtype.fastq2 ${fastq2.name}.fastq;
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14 #else if $jobtype.select == "cl"
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15 mkdir temp_data;
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16 #for $collection_file in $jobtype.collection_files
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17 cp $collection_file temp_data/.;
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18 #end for
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19
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20 $__tool_directory__/ectyper -i temp_data
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21 -d $percent_identity
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22 -l $percent_length
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23 -o "./"; cat ./output/output.csv > results.csv;
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24
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25 GALAXY_URL
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26 #end if
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27
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28
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29 #if $jobtype.select != "cl"
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30 $__tool_directory__/ectyper
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31 #if $jobtype.select == "asm"
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32 -i ${draft.name}.fasta
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33 #else if $jobtype.select == "se"
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34 -i ${fastq1.name}_1.fastq
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35 #else if $jobtype.select == "pe"
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36 -i ${fastq1.name}.fastq,${fastq2.name}.fastq
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37 #end if
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38 -d $percent_identity
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39 -l $percent_length
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40 -o "./"; cat ./output/output.csv > results.csv;
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41 #end if
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42
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43 ]]></command>
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44 <inputs>
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45 <conditional name="jobtype">
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46 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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47 <option value="asm">Genome Assembly</option>
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48 <option value="se">Single-End Reads</option>
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49 <option value="pe">Paired-End Reads</option>
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50 <option value="cl">Collection of Reads</option>
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51 </param>
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52 <when value="asm">
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53 <param name="draft" type="data" format="fasta" label="FASTA" />
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54 </when>
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55 <when value="se">
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56 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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57 </when>
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58 <when value="pe">
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59 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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60 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
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61 </when>
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62 <when value="cl">
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63 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
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64 </when>
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65 </conditional>
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66
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67 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
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68 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
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69
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70 </inputs>
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71 <outputs>
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72 <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/>
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73 </outputs>
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74
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75 <help><![CDATA[
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76
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77 **Usage: ectyper**
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78
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79 **INPUT**
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80
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81 A fasta assembly or single or paired end reads test or data set list of fastqs
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82
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83 **PERCENTIDENTITY**
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84
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85 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
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86
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87 **PERCENTLENGTH**
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88
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89 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
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90
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91 https://github.com/phac-nml/ecoli_serotyping
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92
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93 ]]></help>
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94 </tool>