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comparison sspace.xml @ 1:93fa7ecb5292 draft

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Directly call SSPACE, remove sspace.py and hidden library file output. Use $GALAXY_SLOTS instead of $SSPACE_SITE_OPTIONS. Add readme.rst .
author crs4
date Fri, 21 Feb 2014 04:17:55 -0500
parents b1be94418db9
children bc4451edb703
comparison
equal deleted inserted replaced
0:b1be94418db9 1:93fa7ecb5292
1 <tool id="sspace" name="SSPACE" version="1.0.5"> 1 <tool id="sspace" name="SSPACE" version="1.0.6">
2 <description>scaffolder</description> 2 <description>scaffolder</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0">sspace</requirement> 4 <requirement type="package" version="2.0">sspace</requirement>
5 </requirements> 5 </requirements>
6 6
7 <command interpreter="python"> 7 <command>
8 sspace.py 8 echo "lib1 $reads1 $reads2 $insert $error $orientation" &gt; libraryfile &amp;&amp;
9 \${SSPACE_SITE_OPTIONS:--T 1} 9 perl `which SSPACE_Basic_v2.0.pl` -l libraryfile -s $contigs
10 -c $contigs --r1 $reads1 --r2 $reads2 -i $insert -e $error -o $orientation
11 #if $exten 10 #if $exten
12 -x 11 -x 1
13 #end if 12 #end if
14 #if str($minoverlap) 13 #if str($minoverlap)
15 --minoverlap $minoverlap 14 -m $minoverlap
16 #end if 15 #end if
17 #if str($numofreads) 16 #if str($numofreads)
18 --numofreads $numofreads 17 -o $numofreads
19 #end if 18 #end if
20 #if str($max_trim) 19 #if str($max_trim)
21 -t $max_trim 20 -t $max_trim
22 #end if 21 #end if
23 #if $unpaired 22 #if $unpaired
25 #end if 24 #end if
26 #if str($min_base_ratio) 25 #if str($min_base_ratio)
27 -r $min_base_ratio 26 -r $min_base_ratio
28 #end if 27 #end if
29 #if str($minlink) 28 #if str($minlink)
30 --minlink $minlink 29 -k $minlink
31 #end if 30 #end if
32 #if str($maxratio) 31 #if str($maxratio)
33 --maxratio $maxratio 32 -a $maxratio
34 #end if 33 #end if
35 #if str($contigoverlap) 34 #if str($contigoverlap)
36 --contigoverlap $contigoverlap 35 -n $contigoverlap
37 #end if 36 #end if
38 #if str($mincontig) 37 #if str($mincontig)
39 --mincontig $mincontig 38 -z $mincontig
40 #end if 39 #end if
41 --lib $libraryname --fe $finalevidence --fs $finalscaffolds --lg $logfile --summ $summaryfile 40 -T \${GALAXY_SLOTS:-1} -b sspace
42 </command> 41 </command>
43 42
44 <inputs> 43 <inputs>
45 <param name="contigs" type="data" format="fasta" label="Contigs FASTA file (-s)" /> 44 <param name="contigs" type="data" format="fasta" label="Contigs FASTA file (-s)" />
46 <param name="reads1" type="data" format="fasta,fastq" label="Paired-end reads 1" help="FASTA or FASTQ format" /> 45 <param name="reads1" type="data" format="fasta,fastq" label="Paired-end reads 1" help="FASTA or FASTQ format" />
76 <validator type="in_range" min="0" /> 75 <validator type="in_range" min="0" />
77 </param> 76 </param>
78 </inputs> 77 </inputs>
79 78
80 <outputs> 79 <outputs>
81 <data name="libraryname" hidden="True" format="tabular" label="${tool.name} on ${on_string}: libraryfile" /> 80 <data name="finalevidence" format="txt" label="${tool.name} on ${on_string}: final evidence" from_work_dir="sspace.final.evidence" />
82 <data name="finalevidence" format="txt" label="${tool.name} on ${on_string}: final evidence" /> 81 <data name="finalscaffolds" format="fasta" label="${tool.name} on ${on_string}: final scaffolds" from_work_dir="sspace.final.scaffolds.fasta" />
83 <data name="finalscaffolds" format="fasta" label="${tool.name} on ${on_string}: final scaffolds" /> 82 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="sspace.logfile.txt" />
84 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> 83 <data name="summaryfile" format="txt" label="${tool.name} on ${on_string}: summary" from_work_dir="sspace.summaryfile.txt" />
85 <data name="summaryfile" format="txt" label="${tool.name} on ${on_string}: summary" />
86 </outputs> 84 </outputs>
87 <tests> 85 <tests>
88 86
89 </tests> 87 </tests>
90 <help> 88 <help>