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comparison skesa.xml @ 18:53d82924230b draft

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Uploaded
author estrain
date Thu, 16 Aug 2018 14:54:58 -0400
parents 53297c68021b
children abb622c228c4
comparison
equal deleted inserted replaced
17:53297c68021b 18:53d82924230b
12 #else if $jobtype.select == "se" 12 #else if $jobtype.select == "se"
13 --fastq $fastq1 13 --fastq $fastq1
14 #else if $jobtype.select == "pe" 14 #else if $jobtype.select == "pe"
15 --fastq $fastq1,$fastq2 --use_paired_ends 15 --fastq $fastq1,$fastq2 --use_paired_ends
16 #else if $jobtype.select == "rp" 16 #else if $jobtype.select == "rp"
17 --fastq '{$pairedf.forward}','{$pairedf.reverse}' --use_paired_ends 17 --fastq $jobtype.pairedf.forward,$jobtype.pairedf.reverse --use_paired_ends
18 #end if 18 #end if
19 #if $cores != 0 19 #if $cores != 0
20 --cores $cores 20 --cores $cores
21 #end if 21 #end if
22 --memory $memory > results.skesa.fasta 22 --memory $memory > results.skesa.fasta
23 #end if 23 #end if
24 24
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <conditional name="jobtype"> 27 <conditional name="jobtype">
28 <when value="srr">
29 <param name="srrnum" type="text" label="Sra run number"/>
30 </when>
31 <param name="select" type="select" label="Assembly or FASTQ Reads?"> 28 <param name="select" type="select" label="Assembly or FASTQ Reads?">
32 <option value="sra">SRR number</option> 29 <option value="sra">SRR number</option>
33 <option value="asm">Genome Assembly</option> 30 <option value="asm">Genome Assembly</option>
34 <option value="se">Single-End Reads</option> 31 <option value="se">Single-End Reads</option>
35 <option value="pe">Paired-End Reads (Separate Files)</option> 32 <option value="pe">Paired-End Reads (Separate Files)</option>
36 <option value="rp">Paired-End Reads (Paired Data Set)</option> 33 <option value="rp">Paired-End Reads (Paired Data Set)</option>
37 <option value="cl">Collection of Reads</option> 34 <option value="cl">Collection of Reads</option>
38 </param> 35 </param>
36 <when value="srr">
37 <param name="srrnum" type="text" label="Sra run number"/>
38 </when>
39 <when value="asm"> 39 <when value="asm">
40 <param name="draft" type="data" format="fasta" label="FASTA" /> 40 <param name="draft" type="data" format="fasta" label="FASTA" />
41 </when> 41 </when>
42 <when value="se"> 42 <when value="se">
43 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 43 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
44 </when> 44 </when>
45 <when value="pe"> 45 <when value="pe">
46 <param name="fastq1" type="data" format="fastq" label="FASTQ" /> 46 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
47 <param name="fastq2" type="data" format="fastq" label="FASTQ" /> 47 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
48 </when> 48 </when>
49 <when value="cl"> 49 <when value="cl">
50 <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" /> 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" />
51 </when> 51 </when>
52 <when value="rp"> 52 <when value="rp">
53 <param type="data_collection" collection_type="paired" name="pairedf" format="fastq" label="FASTQS: Must be a paired set of forward and reverse fastq files" /> 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" />
54 </when> 54 </when>
55 </conditional> 55 </conditional>
56 <param name="memory" type="integer" label="Memory available (GB) [integer]" value="16" /> 56 <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" /> 57 <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" /> 58 <param name="kmer" type="integer" label="Minimal kmer length for assembly [default 21] if non are specified " value="0" />