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comparison skesa.xml @ 19:abb622c228c4 draft

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planemo upload commit 1e3adef29c2d50fa89df02d0153e069c4328557e
author cstrittmatter
date Mon, 27 Aug 2018 08:59:02 -0400
parents 53d82924230b
children a368d48a4562
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18:53d82924230b 19:abb622c228c4
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>
4 </requirements> 5 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
6 #if $jobtype.select != "cl" 7
8
9 #if $jobtype.select != "cl"
7 skesa 10 skesa
8 #if $jobtype.select == "srr" 11 #if $jobtype.select == "asm"
9 -sra_run $srrnum
10 #else if $jobtype.select == "asm"
11 --fasta $draft 12 --fasta $draft
12 #else if $jobtype.select == "se" 13 #else if $jobtype.select == "se"
13 --fastq $fastq1 14 --fastq $fastq1
14 #else if $jobtype.select == "pe" 15 #else if $jobtype.select == "pe"
15 --fastq $fastq1,$fastq2 --use_paired_ends 16 --fastq $fastq1,$fastq2 --use_paired_ends
16 #else if $jobtype.select == "rp" 17 #else if $jobtype.select == "rp"
17 --fastq $jobtype.pairedf.forward,$jobtype.pairedf.reverse --use_paired_ends 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
18 #end if 23 #end if
19 #if $cores != 0 24
20 --cores $cores 25
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
21 #end if 37 #end if
22 --memory $memory > results.skesa.fasta
23 #end if
24 38
25 ]]></command> 39 ]]></command>
26 <inputs> 40 <inputs>
27 <conditional name="jobtype"> 41 <conditional name="jobtype">
28 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 42 <param name="select" type="select" label="Assembly or FASTQ Reads?">
29 <option value="sra">SRR number</option>
30 <option value="asm">Genome Assembly</option> 43 <option value="asm">Genome Assembly</option>
31 <option value="se">Single-End Reads</option> 44 <option value="se">Single-End Reads</option>
32 <option value="pe">Paired-End Reads (Separate Files)</option> 45 <option value="pe">Paired-End Reads (Separate Files)</option>
33 <option value="rp">Paired-End Reads (Paired Data Set)</option> 46 <option value="rp">Paired-End Reads (Paired Data Set)</option>
34 <option value="cl">Collection of Reads</option> 47 <option value="cl">Collection of Reads</option>
45 <when value="pe"> 58 <when value="pe">
46 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 59 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
47 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> 60 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
48 </when> 61 </when>
49 <when value="cl"> 62 <when value="cl">
50 <param name="collection_files" type="data_collection" format="fastq" collection_type="list" label="FASTQS: Must be a Data Set list built from multiple fastq files" /> 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" />
51 </when> 64 </when>
52 <when value="rp"> 65 <when value="rp">
53 <param name="pairedf" type="data_collection" collection_type="paired" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" /> 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" />
54 </when> 67 </when>
55 </conditional> 68 </conditional>
56 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" /> 69 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" />
57 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" /> 70 <param name="cores" type="integer" label="Number of cores to use (default all) [integer]" value="0" />
58 <param name="kmer" type="integer" label="Minimal kmer length for assembly [default 21] if non are specified " value="0" />
59 <param name="min_count" type="integer" label="Minimal count for kmers retained for comparing alternate choices [integer]" value="0" />
60 71
61 </inputs> 72 </inputs>
62 <outputs> 73 <outputs>
63 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/> 74 <data format="fasta" label="skesa Results" name="${input.name}.skesa.fasta" from_work_dir="*.fasta"/>
64 </outputs> 75 </outputs>