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comparison ectyper.xml @ 0:4b7f728bcd11 draft

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planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
author cstrittmatter
date Wed, 28 Mar 2018 14:05:50 -0400
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1 <tool id="ectyper" name="ectyper" version="0.1">
2 <requirements>
3 <requirement type="package" version="0.1">ectyper</requirement>
4 <requirement type="package" version="3.5">python</requirement>
5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[
7 #if $jobtype.select == "asm"
8 ln -s $jobtype.draft ${draft.name}.fasta;
9 #else if $jobtype.select == "se"
10 ln -s $jobtype.fastq1 ${fastq1.name}_1.fastq;
11 #else if $jobtype.select == "pe"
12 ln -s $jobtype.fastq1 ${fastq1.name}.fastq;
13 ln -s $jobtype.fastq2 ${fastq2.name}.fastq;
14 #else if $jobtype.select == "cl"
15 mkdir temp_data;
16 #for $collection_file in $jobtype.collection_files
17 cp $collection_file temp_data/.;
18 #end for
19
20 $__tool_directory__/ectyper -i temp_data
21 -d $percent_identity
22 -l $percent_length
23 -o "./"; cat ./output/output.csv > results.csv;
24
25 GALAXY_URL
26 #end if
27
28
29 #if $jobtype.select != "cl"
30 $__tool_directory__/ectyper
31 #if $jobtype.select == "asm"
32 -i ${draft.name}.fasta
33 #else if $jobtype.select == "se"
34 -i ${fastq1.name}_1.fastq
35 #else if $jobtype.select == "pe"
36 -i ${fastq1.name}.fastq,${fastq2.name}.fastq
37 #end if
38 -d $percent_identity
39 -l $percent_length
40 -o "./"; cat ./output/output.csv > results.csv;
41 #end if
42
43 ]]></command>
44 <inputs>
45 <conditional name="jobtype">
46 <param name="select" type="select" label="Assembly or FASTQ Reads?">
47 <option value="asm">Genome Assembly</option>
48 <option value="se">Single-End Reads</option>
49 <option value="pe">Paired-End Reads</option>
50 <option value="cl">Collection of Reads</option>
51 </param>
52 <when value="asm">
53 <param name="draft" type="data" format="fasta" label="FASTA" />
54 </when>
55 <when value="se">
56 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
57 </when>
58 <when value="pe">
59 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
60 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
61 </when>
62 <when value="cl">
63 <param type="data_collection" name="collection_files" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
64 </when>
65 </conditional>
66
67 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
68 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
69
70 </inputs>
71 <outputs>
72 <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/>
73 </outputs>
74
75 <help><![CDATA[
76
77 **Usage: ectyper**
78
79 **INPUT**
80
81 A fasta assembly or single or paired end reads test or data set list of fastqs
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 https://github.com/phac-nml/ecoli_serotyping
92
93 ]]></help>
94 </tool>