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comparison ectyper.xml @ 22:6633619837ad draft default tip

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planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
author charles_s_test
date Mon, 12 Mar 2018 09:52:17 -0400
parents 85391c6aa2c5
children
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21:85391c6aa2c5 22:6633619837ad
1 <tool id="ectyper" name="ectyper" version="0.1"> 1 <tool id="ectyper" name="ectyper" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1">ectyper</requirement> 3 <requirement type="package" version="0.1">ectyper</requirement>
4 <requirement type="package" version="3.5">python</requirement>
4 </requirements> 5 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
6 #if $jobtype.select == "asm" 7 #if $jobtype.select == "asm"
7 ln -s $jobtype.draft sample.fasta; 8 ln -s $jobtype.draft ${draft.name}.fasta;
8 #else if $jobtype.select == "se" 9 #else if $jobtype.select == "se"
9 ln -s $jobtype.fastq1 sample_1.fastq; 10 ln -s $jobtype.fastq1 ${fastq1.name}_1.fastq;
10 #else if $jobtype.select == "pe" 11 #else if $jobtype.select == "pe"
11 ln -s $jobtype.fastq1 sample_1.fastq; 12 ln -s $jobtype.fastq1 ${fastq1.name}.fastq;
12 ln -s $jobtype.fastq2 sample_2.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
13 #end if 26 #end if
14 27
15 $__tool_directory__/ectyper 28
29 #if $jobtype.select != "cl"
30 $__tool_directory__/ectyper
16 #if $jobtype.select == "asm" 31 #if $jobtype.select == "asm"
17 -i sample.fasta 32 -i ${draft.name}.fasta
18 #else if $jobtype.select == "se" 33 #else if $jobtype.select == "se"
19 -i sample_1.fastq 34 -i ${fastq1.name}_1.fastq
20 #else if $jobtype.select == "pe" 35 #else if $jobtype.select == "pe"
21 -i sample_1.fastq sample_2.fastq 36 -i ${fastq1.name}.fastq,${fastq2.name}.fastq
22 #end if 37 #end if
23 -d $percent_identity 38 -d $percent_identity
24 -l $percent_length 39 -l $percent_length
25 -o "./"; cat ./output/output.csv > results.csv; 40 -o "./"; cat ./output/output.csv > results.csv;
41 #end if
26 42
27 ]]></command> 43 ]]></command>
28 <inputs> 44 <inputs>
29 <conditional name="jobtype"> 45 <conditional name="jobtype">
30 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 46 <param name="select" type="select" label="Assembly or FASTQ Reads?">
31 <option value="asm">Genome Assembly</option> 47 <option value="asm">Genome Assembly</option>
32 <option value="se">Single-End Reads</option> 48 <option value="se">Single-End Reads</option>
33 <option value="pe">Paired-End Reads</option> 49 <option value="pe">Paired-End Reads</option>
50 <option value="cl">Collection of Reads</option>
34 </param> 51 </param>
35 <when value="asm"> 52 <when value="asm">
36 <param name="draft" type="data" format="fasta" label="FASTA" /> 53 <param name="draft" type="data" format="fasta" label="FASTA" />
37 </when> 54 </when>
38 <when value="se"> 55 <when value="se">
40 </when> 57 </when>
41 <when value="pe"> 58 <when value="pe">
42 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 59 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
43 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> 60 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
44 </when> 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>
45 </conditional> 65 </conditional>
46 66
47 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" /> 67 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
48 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" /> 68 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
49 69
50 </inputs> 70 </inputs>
51 <outputs> 71 <outputs>
56 76
57 **Usage: ectyper** 77 **Usage: ectyper**
58 78
59 **INPUT** 79 **INPUT**
60 80
61 A fasta assembly or single or paired end reads 81 A fasta assembly or single or paired end reads test or data set list of fastqs
62 82
63 **PERCENTIDENTITY** 83 **PERCENTIDENTITY**
64 84
65 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%. 85 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
66 86