spades: spades.xml annotate

annotate spades.xml @ 5:fbe9ee43bc13 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9

author	iuc
date	Tue, 11 Dec 2018 13:34:47 -0500
parents	2682640145c8
children	e246a51e600c

rev	line source
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1">
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	2 <description>genome assembler for regular and single-cell projects</description>
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	3 <macros>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	4 <import>macros.xml</import>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	5 </macros>
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	6 <requirements>
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	7 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	8 </requirements>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	9 <stdio>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	10 <exit_code range="1:" />
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	11 <regex match="Cannot allocate memory"
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	12 source="stdout"
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	13 level="fatal_oom"
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	14 description="Out of memory error occurred" />
3 f987a1058654 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e iuc parents: 2 diff changeset	15 <regex match="The reads contain too many k-mers to fit into available memory"
f987a1058654 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e iuc parents: 2 diff changeset	16 source="stdout"
f987a1058654 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e iuc parents: 2 diff changeset	17 level="fatal_oom"
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	18 description="Out of memory error occurred" />
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	19 </stdio>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	20 <command>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	21 <![CDATA[
c7cae3a5e8d7 planemo upload nml parents: diff changeset	22 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	23
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	24 if [[ -n \$GALAXY_MEMORY_MB ]]; then
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	25 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	26 fi &&
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	27
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	28 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	29 #if not $kmer_choice.auto_kmer_choice:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	30 -k "$kmer_choice.kmers"
c7cae3a5e8d7 planemo upload nml parents: diff changeset	31 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	32 #if $cov.state == "auto":
c7cae3a5e8d7 planemo upload nml parents: diff changeset	33 --cov-cutoff 'auto'
c7cae3a5e8d7 planemo upload nml parents: diff changeset	34 #elif $cov.state == "value":
c7cae3a5e8d7 planemo upload nml parents: diff changeset	35 --cov-cutoff '$cov.cutoff'
c7cae3a5e8d7 planemo upload nml parents: diff changeset	36 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	37 $iontorrent
c7cae3a5e8d7 planemo upload nml parents: diff changeset	38 ## Sequence files, libraries
c7cae3a5e8d7 planemo upload nml parents: diff changeset	39 #for $i, $library in enumerate( $libraries, start=1 )
c7cae3a5e8d7 planemo upload nml parents: diff changeset	40 #if str( $library.lib_type ) == "paired_end":
c7cae3a5e8d7 planemo upload nml parents: diff changeset	41 #set prefix = 'pe'
c7cae3a5e8d7 planemo upload nml parents: diff changeset	42 #elif str( $library.lib_type ) == "mate_paired":
c7cae3a5e8d7 planemo upload nml parents: diff changeset	43 #set prefix = 'mp'
c7cae3a5e8d7 planemo upload nml parents: diff changeset	44 #elif str( $library.lib_type ) == "nxmate_paired":
c7cae3a5e8d7 planemo upload nml parents: diff changeset	45 #set prefix = 'nxmate'
c7cae3a5e8d7 planemo upload nml parents: diff changeset	46 #else:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	47 #set prefix = 'hqmp'
c7cae3a5e8d7 planemo upload nml parents: diff changeset	48 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	49 --$prefix$i-$library.orientation
c7cae3a5e8d7 planemo upload nml parents: diff changeset	50 #for $file in $library.files
c7cae3a5e8d7 planemo upload nml parents: diff changeset	51 #if $file.file_type.type == "separate"
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	52 --$prefix$i-1 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.fwd_reads
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	53 --$prefix$i-2 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.rev_reads
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	54 #elif $file.file_type.type == "interleaved"
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	55 --$prefix$i-12 $file.file_type.interleaved_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.interleaved_reads
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	56 #elif $file.file_type.type == "merged"
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	57 --$prefix$i-m $file.file_type.merged_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.merged_reads
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	58 #elif $file.file_type.type == "unpaired"
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	59 --$prefix$i-s $file.file_type.unpaired_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.unpaired_reads
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	60 #elif $file.file_type.type == "paired-collection"
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	61 --$prefix$i-1 $file.file_type.fastq_collection.forward.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.forward
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	62 --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.reverse
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	63 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	64 #end for
c7cae3a5e8d7 planemo upload nml parents: diff changeset	65 #end for
c7cae3a5e8d7 planemo upload nml parents: diff changeset	66 #for $read in $pacbio_reads:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	67 #if $read:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	68 --pacbio fastq:$read
c7cae3a5e8d7 planemo upload nml parents: diff changeset	69 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	70 #end for
c7cae3a5e8d7 planemo upload nml parents: diff changeset	71 #for $read in $nanopore_reads:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	72 #if $read:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	73 --nanopore fastq:$read
c7cae3a5e8d7 planemo upload nml parents: diff changeset	74 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	75 #end for
c7cae3a5e8d7 planemo upload nml parents: diff changeset	76 #for $read in $sanger_reads:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	77 #if $read:
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	78 --sanger $read.extension.replace('fastqsanger', 'fastq'):$read
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	79 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	80 #end for
c7cae3a5e8d7 planemo upload nml parents: diff changeset	81 #for $contig in $trusted_contigs:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	82 #if $contig:
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	83 --trusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	84 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	85 #end for
c7cae3a5e8d7 planemo upload nml parents: diff changeset	86 #for $contig in $untrusted_contigs:
c7cae3a5e8d7 planemo upload nml parents: diff changeset	87 #if $contig:
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	88 --untrusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	89 #end if
c7cae3a5e8d7 planemo upload nml parents: diff changeset	90 #end for
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	91 && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats'
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	92 && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats'
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	93 ]]>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	94 </command>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	95
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	96 <configfiles>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	97 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	98 import sys,re
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	99 search_str = r'^>(NODE\|\S+)_(\d+)(?:_\|\s)length_(\d+)_cov_(\d+\.\d).*\$'
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	100 replace_str = r'\1_\2\t\3\t\4'
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	101 cmd = re.compile(search_str)
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	102 sys.stdout.write('#name\tlength\tcoverage\n')
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	103 for i,line in enumerate(sys.stdin):
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	104 if cmd.match(line):
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	105 sys.stdout.write(cmd.sub(replace_str,line))
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	106 ]]>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	107 </configfile>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	108 </configfiles>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	109
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	110 <inputs>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	111 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	112 <option value="false">No</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	113 <option value="true">Yes</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	114 </param>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	115 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	116 <param argument="--careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	117 <conditional name="kmer_choice">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	118 <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	119 <when value="false">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	120 <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	121 </when>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	122 <when value="true" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	123 </conditional>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	124 <conditional name="cov">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	125 <param label="Coverage Cutoff" name="state" type="select">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	126 <option value="off">Off</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	127 <option value="value">User Specific</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	128 <option value="auto">Auto</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	129 </param>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	130 <when value="off" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	131 <when value="value">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	132 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	133 </when>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	134 <when value="auto" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	135 </conditional>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	136 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	137 <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" max="9" name="libraries" title="Libraries">
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	138 <param label="Library type" name="lib_type" type="select">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	139 <option value="paired_end">Paired-end / Single reads</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	140 <option value="mate_paired">Mate pairs</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	141 <option value="high_mate_paired">High Quality Mate pairs</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	142 <option value="nxmate_paired">Lucigen NxMate pairs</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	143 </param>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	144 <param label="Orientation" name="orientation" type="select">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	145 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	146 <option value="rf"><![CDATA[<- -> (rf)]]></option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	147 <option value="ff"><![CDATA[-> -> (ff)]]></option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	148 </param>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	149 <repeat min="1" name="files" title="Files">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	150 <conditional name="file_type">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	151 <param label="Select file format" name="type" type="select">
c7cae3a5e8d7 planemo upload nml parents: diff changeset	152 <option value="separate">Separate input files</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	153 <option value="interleaved">Interleaved files</option>
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	154 <option value="merged">Merged files</option>
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	155 <option value="unpaired">Unpaired/Single reads</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	156 <option value="paired-collection">Paired List Collection</option>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	157 </param>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	158 <when value="separate">
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	159 <param format="@INTYPES@" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	160 <param format="@INTYPES@" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	161 </when>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	162 <when value="interleaved">
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	163 <param format="@INTYPES@" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	164 </when>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	165 <when value="merged">
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	166 <param format="@INTYPES@" help="FASTQ format" label="Merged paired reads" name="merged_reads" type="data" />
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	167 </when>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	168 <when value="unpaired">
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	169 <param format="@INTYPES@" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	170 </when>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	171 <when value="paired-collection">
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	172 <param collection_type="paired" format="@INTYPES@" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	173 </when>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	174 </conditional>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	175 </repeat>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	176 </repeat>
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	177 <param optional="true" format="@INTYPES@" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	178 <param optional="true" format="@INTYPES@" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	179 <param optional="true" format="@INTYPES@" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	180 <param optional="true" format="@INTYPES@" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	181 <param optional="true" format="@INTYPES@" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	182 <param name="contig_graph_out" type="boolean" checked="False" label="Output final assembly graph (contigs)?" help="Will output the final assembly graph (contigs) in fastg format for visualisation" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	183 <param name="scaffold_graph_out" type="boolean" checked="False" label="Output final assembly graph with scaffolds?" help="Will output the final assembly graph with scaffold information in gfa format for visualisation" />
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	184 </inputs>
1 40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	185
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	186 <outputs>
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	187 <data format="tabular" label="${tool.name} on ${on_string}: contig stats" name="out_contig_stats" >
1 40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	188 <actions>
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	189 <action name="column_names" type="metadata" default="name,length,coverage"/>
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	190 </actions>
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	191 </data>
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	192 <data format="tabular" label="${tool.name} on ${on_string}: scaffold stats" name="out_scaffold_stats" >
1 40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	193 <actions>
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	194 <action name="column_names" type="metadata" default="name,length,coverage"/>
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	195 </actions>
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	196 </data>
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	197 <data format="fasta" from_work_dir="contigs.fasta" label="${tool.name} on ${on_string}: contigs (fasta)" name="out_contigs" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	198 <data format="fasta" from_work_dir="scaffolds.fasta" label="${tool.name} on ${on_string}: scaffolds (fasta)" name="out_scaffolds" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	199 <data format="txt" from_work_dir="spades.log" label="${tool.name} on ${on_string}: log" name="out_log" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	200 <data format="txt" from_work_dir="assembly_graph.fastg" label="${tool.name} on ${on_string}: assembly graph" name="contig_graph">
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	201 <filter>contig_graph_out</filter>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	202 </data>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	203 <data format="txt" from_work_dir="assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: assembly graph with scaffolds" name="scaffold_graph">
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	204 <filter>scaffold_graph_out</filter>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	205 </data>
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	206 </outputs>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	207 <tests>
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	208 <test> <!-- Test 1 - basic test with k=33 -->
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	209 <param name="sc" value="false" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	210 <param name="careful" value="false" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	211 <param name="kmers" value="33" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	212 <param name="lib_type" value="paired_end" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	213 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	214 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	215 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
1 40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	216 <output name="out_contig_stats">
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	217 <assert_contents>
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	218 <has_text_matching expression="NODE_1\t1000"/>
1 40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	219 </assert_contents>
40eedd16a4ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 0 diff changeset	220 </output>
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	221 </test>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	222 <test> <!-- Test 2 - basic test with k=33 fasta input -->
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	223 <param name="sc" value="false" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	224 <param name="onlyassembler" value="true"/>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	225 <param name="careful" value="false" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	226 <param name="kmers" value="33" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	227 <param name="lib_type" value="paired_end" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	228 <param ftype="fasta" name="fwd_reads" value="ecoli_1K_1.fasta" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	229 <param ftype="fasta" name="rev_reads" value="ecoli_1K_2.fasta" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	230 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	231 <output name="out_contig_stats">
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	232 <assert_contents>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	233 <has_text_matching expression="NODE_1\t1000"/>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	234 </assert_contents>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	235 </output>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	236 </test>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	237 <test> <!-- Test 3 - basic test with k=33 and gzipped input -->
4 2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	238 <param name="sc" value="false" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	239 <param name="careful" value="false" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	240 <param name="kmers" value="33" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	241 <param name="lib_type" value="paired_end" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	242 <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	243 <param ftype="fastq.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	244 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	245 <output name="out_contig_stats">
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	246 <assert_contents>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	247 <has_text_matching expression="NODE_1\t1000"/>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	248 </assert_contents>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	249 </output>
2682640145c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 3 diff changeset	250 </test>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	251 <test> <!-- Test 4 - auto k -->
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	252 <param name="sc" value="false" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	253 <param name="careful" value="false" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	254 <param name="auto_kmer_choice" value="true" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	255 <param name="lib_type" value="paired_end" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	256 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	257 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	258 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	259 </test>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	260 <test> <!-- Test 5 - k=77 -->
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	261 <param name="sc" value="false" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	262 <param name="careful" value="false" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	263 <param name="kmers" value="77" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	264 <param name="lib_type" value="paired_end" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	265 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	266 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	267 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
c7cae3a5e8d7 planemo upload nml parents: diff changeset	268 </test>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	269 <test> <!-- Test 6 - test for extra graph outputs -->
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	270 <param name="sc" value="false" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	271 <param name="careful" value="false" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	272 <param name="kmers" value="33" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	273 <param name="lib_type" value="paired_end" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	274 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	275 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	276 <param name="contig_graph_out" value="true" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	277 <param name="scaffold_graph_out" value="true" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	278 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	279 <output name="out_contig_stats">
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	280 <assert_contents>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	281 <has_text_matching expression="NODE_1\t1000"/>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	282 </assert_contents>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	283 </output>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	284 <output name="contig_graph">
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	285 <assert_contents>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	286 <has_text text=">EDGE_"/>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	287 </assert_contents>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	288 </output>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	289 <output name="scaffold_graph">
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	290 <assert_contents>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	291 <has_text text="NODE_"/>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	292 </assert_contents>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	293 </output>
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	294 </test>
5 fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	295 <test> <!-- Test 7 - basic test with k=33 and fastsanger input -->
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	296 <param name="sc" value="false" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	297 <param name="careful" value="false" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	298 <param name="kmers" value="33" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	299 <param name="lib_type" value="paired_end" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	300 <param ftype="fastqsanger" name="fwd_reads" value="ecoli_1K_1.fq" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	301 <param ftype="fastqsanger" name="rev_reads" value="ecoli_1K_2.fq" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	302 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	303 <output name="out_contig_stats">
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	304 <assert_contents>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	305 <has_text_matching expression="NODE_1\t1000"/>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	306 </assert_contents>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	307 </output>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	308 </test>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	309 <test> <!-- Test 8 - basic test with k=33 and fastsanger.gz input -->
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	310 <param name="sc" value="false" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	311 <param name="careful" value="false" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	312 <param name="kmers" value="33" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	313 <param name="lib_type" value="paired_end" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	314 <param ftype="fastqsanger.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	315 <param ftype="fastqsanger.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	316 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	317 <output name="out_contig_stats">
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	318 <assert_contents>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	319 <has_text_matching expression="NODE_1\t1000"/>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	320 </assert_contents>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	321 </output>
fbe9ee43bc13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 4 diff changeset	322 </test>
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	323 </tests>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	324 <help>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	325 <![CDATA[
c7cae3a5e8d7 planemo upload nml parents: diff changeset	326 What it does
c7cae3a5e8d7 planemo upload nml parents: diff changeset	327
c7cae3a5e8d7 planemo upload nml parents: diff changeset	328 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
c7cae3a5e8d7 planemo upload nml parents: diff changeset	329
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	330 This wrapper runs SPAdes, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	331
c7cae3a5e8d7 planemo upload nml parents: diff changeset	332 License
c7cae3a5e8d7 planemo upload nml parents: diff changeset	333
c7cae3a5e8d7 planemo upload nml parents: diff changeset	334 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
c7cae3a5e8d7 planemo upload nml parents: diff changeset	335
c7cae3a5e8d7 planemo upload nml parents: diff changeset	336 This wrapper is copyrighted by Philip Mabon and is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
c7cae3a5e8d7 planemo upload nml parents: diff changeset	337
c7cae3a5e8d7 planemo upload nml parents: diff changeset	338 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
c7cae3a5e8d7 planemo upload nml parents: diff changeset	339
c7cae3a5e8d7 planemo upload nml parents: diff changeset	340 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
c7cae3a5e8d7 planemo upload nml parents: diff changeset	341
c7cae3a5e8d7 planemo upload nml parents: diff changeset	342 Acknowledgments
c7cae3a5e8d7 planemo upload nml parents: diff changeset	343
c7cae3a5e8d7 planemo upload nml parents: diff changeset	344 Original wrapper developed by Lionel Guy.
c7cae3a5e8d7 planemo upload nml parents: diff changeset	345
c7cae3a5e8d7 planemo upload nml parents: diff changeset	346 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
c7cae3a5e8d7 planemo upload nml parents: diff changeset	347
c7cae3a5e8d7 planemo upload nml parents: diff changeset	348 Nicola Soranzo fixed various bugs.
2 210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	349
210b731002af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 1 diff changeset	350 Simon Gladman added fastg optional outputs.
0 c7cae3a5e8d7 planemo upload nml parents: diff changeset	351 ]]>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	352 </help>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	353 <citations>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	354 <citation type="doi">10.1089/cmb.2012.0021</citation>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	355 </citations>
c7cae3a5e8d7 planemo upload nml parents: diff changeset	356 </tool>

Mercurial > repos > nml > spades

annotate spades.xml @ 5:fbe9ee43bc13 draft