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comparison skesa.xml @ 20:a368d48a4562 draft

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planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty
author cstrittmatter
date Thu, 13 Sep 2018 09:34:22 -0400
parents abb622c228c4
children 8bafd3d18864
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19:abb622c228c4 20:a368d48a4562
1 <tool id="skesa" name="skesa" version="0.1"> 1 <tool id="skesa" name="skesa" version="0.1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="2.2">skesa</requirement> 3 <requirement type="package" version="2.2">skesa</requirement>
4 <requirement type="package" >python</requirement>
5 </requirements> 4 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
7 6 #if $jobtype.select != "cl"
8
9 #if $jobtype.select != "cl"
10 skesa 7 skesa
11 #if $jobtype.select == "asm" 8 #if $jobtype.select == "asm"
12 --fasta $draft 9 --fasta $draft
13 #else if $jobtype.select == "se" 10 #else if $jobtype.select == "se"
14 --fastq $fastq1 11 --fastq $fastq1
15 #else if $jobtype.select == "pe" 12 #else if $jobtype.select == "pe"
16 --fastq $fastq1,$fastq2 --use_paired_ends 13 --fastq $fastq1,$fastq2 --use_paired_ends
17 #else if $jobtype.select == "rp"
18 --fastq $jobtype.pairedf.forward,$jobtype.pairedf.reverse --use_paired_ends
19 #if $cores != 0
20 --cores $cores
21 #end if
22 --memory $memory > results.skesa.fasta
23 #end if 14 #end if
24 15 #if $cores != 0
25 16 --cores $cores
26 #if $jobtype.select == "cl"
27
28 #set $pathOuput = 0
29 mkdir temp_data;
30 #for $collection_file in $jobtype.collection_files
31 #silent sys.stderr.write($collection_file+"\n")
32 cp $collection_file temp_data/.;
33
34 #end for
35
36
37 #end if 17 #end if
18 --memory $memory > results.skesa.fasta
19 #end if
38 20
39 ]]></command> 21 ]]></command>
40 <inputs> 22 <inputs>
41 <conditional name="jobtype"> 23 <conditional name="jobtype">
42 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 24 <param name="select" type="select" label="Assembly or FASTQ Reads?">
43 <option value="asm">Genome Assembly</option> 25 <option value="asm">Genome Assembly</option>
44 <option value="se">Single-End Reads</option> 26 <option value="se">Single-End Reads</option>
45 <option value="pe">Paired-End Reads (Separate Files)</option> 27 <option value="pe">Paired-End Reads (Separate Files)</option>
46 <option value="rp">Paired-End Reads (Paired Data Set)</option>
47 <option value="cl">Collection of Reads</option>
48 </param> 28 </param>
49 <when value="srr">
50 <param name="srrnum" type="text" label="Sra run number"/>
51 </when>
52 <when value="asm"> 29 <when value="asm">
53 <param name="draft" type="data" format="fasta" label="FASTA" /> 30 <param name="draft" type="data" format="fasta" label="FASTA" />
54 </when> 31 </when>
55 <when value="se"> 32 <when value="se">
56 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 33 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
57 </when> 34 </when>
58 <when value="pe"> 35 <when value="pe">
59 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 36 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
60 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> 37 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
61 </when> 38 </when>
62 <when value="cl">
63 <param name="collection_files" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" label="FASTQS: Must be a Data Set list built from multiple fastq files" />
64 </when>
65 <when value="rp">
66 <param name="pairedf" type="data_collection" collection_type="paired" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" />
67 </when>
68 </conditional> 39 </conditional>
69 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" /> 40 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
70 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" /> 41 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
71 42
72 </inputs> 43 </inputs>
73 <outputs> 44 <outputs>
74 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/> 45 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
75 </outputs> 46 </outputs>
76 47