spades: spades.xml annotate

annotate spades.xml @ 13:b7829778729f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 4125a5c59656970247dea551c424171bb7623749"

author	iuc
date	Mon, 20 Sep 2021 09:55:41 +0000
parents	1796ea206dec
children	74f20c988994

rev	line source
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	1 <tool id="spades" name="SPAdes" version="@TOOL_VERSION@+galaxy1">
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	2 <description>genome assembler for regular and single-cell projects</description>
12 1796ea206dec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95" iuc parents: 10 diff changeset	3 <xrefs>
1796ea206dec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95" iuc parents: 10 diff changeset	4 <xref type="bio.tools">spades</xref>
1796ea206dec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95" iuc parents: 10 diff changeset	5 </xrefs>
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	6 <macros>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	7 <import>macros.xml</import>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	8 </macros>
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	9 <requirements>
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	10 <requirement type="package" version="@TOOL_VERSION@">spades</requirement>
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	11 </requirements>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	12 <stdio>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	13 <exit_code range="1:" />
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	14 <regex match="Cannot allocate memory"
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	15 source="stdout"
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	16 level="fatal_oom"
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	17 description="Out of memory error occurred" />
8 884dc0264950 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e iuc parents: 7 diff changeset	18 <regex match="The reads contain too many k-mers to fit into available memory"
884dc0264950 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e iuc parents: 7 diff changeset	19 source="stdout"
884dc0264950 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 681797a4ef698cba492fd19c57c10f7c807e885e iuc parents: 7 diff changeset	20 level="fatal_oom"
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	21 description="Out of memory error occurred" />
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	22 </stdio>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	23 <command>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	24 <![CDATA[
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	25 ## 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
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	26
12 1796ea206dec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a66345b894a128f7cb44876cc9a51f48c5213d95" iuc parents: 10 diff changeset	27 if [ -n "\$GALAXY_MEMORY_MB" ]; then
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	28 GALAXY_MEMORY_GB=\$(( GALAXY_MEMORY_MB / 1024 ));
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	29 fi &&
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	30
13 b7829778729f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 4125a5c59656970247dea551c424171bb7623749" iuc parents: 12 diff changeset	31 spades.py -o . --tmp-dir "\${TMPDIR:-.}" --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16} -m \${GALAXY_MEMORY_GB:-250}
4 35cb17bd8bf9 planemo upload commit ba4e93c036a072d6aac883bc1aba55e26256498c nml parents: 3 diff changeset	32 #if not $kmer_choice.auto_kmer_choice:
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	33 -k "$kmer_choice.kmers"
3 6dff6ed33cd7 planemo upload commit b8b20b735c418c2f2086a6aa48a7e36e34f80753 nml parents: 2 diff changeset	34 #end if
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	35 #if $cov.state == "auto":
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	36 --cov-cutoff 'auto'
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	37 #elif $cov.state == "value":
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	38 --cov-cutoff '$cov.cutoff'
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	39 #end if
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	40 $iontorrent
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	41 ## Sequence files, libraries
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	42 #for $i, $library in enumerate( $libraries, start=1 )
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	43 #if str( $library.lib_type ) == "paired_end":
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	44 #set prefix = 'pe'
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	45 #elif str( $library.lib_type ) == "mate_paired":
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	46 #set prefix = 'mp'
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	47 #elif str( $library.lib_type ) == "nxmate_paired":
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	48 #set prefix = 'nxmate'
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	49 #else:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	50 #set prefix = 'hqmp'
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	51 #end if
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	52 --$prefix$i-$library.orientation
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	53 #for $file in $library.files
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	54 #if $file.file_type.type == "separate"
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	55 --$prefix$i-1 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.fwd_reads
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	56 --$prefix$i-2 $file.file_type.fwd_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.rev_reads
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	57 #elif $file.file_type.type == "interleaved"
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	58 --$prefix$i-12 $file.file_type.interleaved_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.interleaved_reads
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	59 #elif $file.file_type.type == "merged"
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	60 --$prefix$i-m $file.file_type.merged_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.merged_reads
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	61 #elif $file.file_type.type == "unpaired"
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	62 --$prefix$i-s $file.file_type.unpaired_reads.extension.replace('fastqsanger', 'fastq'):$file.file_type.unpaired_reads
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	63 #elif $file.file_type.type == "paired-collection"
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	64 --$prefix$i-1 $file.file_type.fastq_collection.forward.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.forward
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	65 --$prefix$i-2 $file.file_type.fastq_collection.reverse.extension.replace('fastqsanger', 'fastq'):$file.file_type.fastq_collection.reverse
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	66 #end if
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	67 #end for
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	68 #end for
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	69 #for $read in $pacbio_reads:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	70 #if $read:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	71 --pacbio fastq:$read
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	72 #end if
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	73 #end for
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	74 #for $read in $nanopore_reads:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	75 #if $read:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	76 --nanopore fastq:$read
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	77 #end if
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	78 #end for
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	79 #for $read in $sanger_reads:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	80 #if $read:
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	81 --sanger $read.extension.replace('fastqsanger', 'fastq'):$read
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	82 #end if
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	83 #end for
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	84 #for $contig in $trusted_contigs:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	85 #if $contig:
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	86 --trusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	87 #end if
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	88 #end for
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	89 #for $contig in $untrusted_contigs:
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	90 #if $contig:
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	91 --untrusted-contigs $contig.extension.replace('fastqsanger', 'fastq'):$contig
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	92 #end if
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	93 #end for
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	94 && python '$write_tsv_script' < contigs.fasta > '$out_contig_stats'
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	95 && python '$write_tsv_script' < scaffolds.fasta > '$out_scaffold_stats'
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	96 ]]>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	97 </command>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	98
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	99 <configfiles>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	100 <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	101 import sys,re
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	102 search_str = r'^>(NODE\|\S+)_(\d+)(?:_\|\s)length_(\d+)_cov_(\d+\.\d).*\$'
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	103 replace_str = r'\1_\2\t\3\t\4'
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	104 cmd = re.compile(search_str)
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	105 sys.stdout.write('#name\tlength\tcoverage\n')
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	106 for i,line in enumerate(sys.stdin):
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	107 if cmd.match(line):
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	108 sys.stdout.write(cmd.sub(replace_str,line))
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	109 ]]>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	110 </configfile>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	111 </configfiles>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	112
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	113 <inputs>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	114 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	115 <option value="false">No</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	116 <option value="true">Yes</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	117 </param>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	118 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	119 <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" />
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	120 <conditional name="kmer_choice">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	121 <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" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	122 <when value="false">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	123 <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" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	124 </when>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	125 <when value="true" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	126 </conditional>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	127 <conditional name="cov">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	128 <param label="Coverage Cutoff" name="state" type="select">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	129 <option value="off">Off</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	130 <option value="value">User Specific</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	131 <option value="auto">Auto</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	132 </param>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	133 <when value="off" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	134 <when value="value">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	135 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	136 </when>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	137 <when value="auto" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	138 </conditional>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	139 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	140 <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">
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	141 <param label="Library type" name="lib_type" type="select">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	142 <option value="paired_end">Paired-end / Single reads</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	143 <option value="mate_paired">Mate pairs</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	144 <option value="high_mate_paired">High Quality Mate pairs</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	145 <option value="nxmate_paired">Lucigen NxMate pairs</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	146 </param>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	147 <param label="Orientation" name="orientation" type="select">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	148 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	149 <option value="rf"><![CDATA[<- -> (rf)]]></option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	150 <option value="ff"><![CDATA[-> -> (ff)]]></option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	151 </param>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	152 <repeat min="1" name="files" title="Files">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	153 <conditional name="file_type">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	154 <param label="Select file format" name="type" type="select">
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	155 <option value="separate">Separate input files</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	156 <option value="interleaved">Interleaved files</option>
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	157 <option value="merged">Merged files</option>
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	158 <option value="unpaired">Unpaired/Single reads</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	159 <option value="paired-collection">Paired List Collection</option>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	160 </param>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	161 <when value="separate">
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	162 <param format="@INTYPES@" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	163 <param format="@INTYPES@" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	164 </when>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	165 <when value="interleaved">
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	166 <param format="@INTYPES@" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	167 </when>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	168 <when value="merged">
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	169 <param format="@INTYPES@" help="FASTQ format" label="Merged paired reads" name="merged_reads" type="data" />
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	170 </when>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	171 <when value="unpaired">
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	172 <param format="@INTYPES@" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	173 </when>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	174 <when value="paired-collection">
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	175 <param collection_type="paired" format="@INTYPES@" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	176 </when>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	177 </conditional>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	178 </repeat>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	179 </repeat>
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	180 <param optional="true" format="@INTYPES@" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	181 <param optional="true" format="@INTYPES@" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	182 <param optional="true" format="@INTYPES@" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	183 <param optional="true" format="@INTYPES@" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	184 <param optional="true" format="@INTYPES@" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	185 <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" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	186 <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" />
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	187 </inputs>
6 65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	188
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	189 <outputs>
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	190 <data format="tabular" label="${tool.name} on ${on_string}: contig stats" name="out_contig_stats" >
6 65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	191 <actions>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	192 <action name="column_names" type="metadata" default="name,length,coverage"/>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	193 </actions>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	194 </data>
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	195 <data format="tabular" label="${tool.name} on ${on_string}: scaffold stats" name="out_scaffold_stats" >
6 65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	196 <actions>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	197 <action name="column_names" type="metadata" default="name,length,coverage"/>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	198 </actions>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	199 </data>
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	200 <data format="fasta" from_work_dir="contigs.fasta" label="${tool.name} on ${on_string}: contigs (fasta)" name="out_contigs" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	201 <data format="fasta" from_work_dir="scaffolds.fasta" label="${tool.name} on ${on_string}: scaffolds (fasta)" name="out_scaffolds" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	202 <data format="txt" from_work_dir="spades.log" label="${tool.name} on ${on_string}: log" name="out_log" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	203 <data format="txt" from_work_dir="assembly_graph.fastg" label="${tool.name} on ${on_string}: assembly graph" name="contig_graph">
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	204 <filter>contig_graph_out</filter>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	205 </data>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	206 <data format="txt" from_work_dir="assembly_graph_with_scaffolds.gfa" label="${tool.name} on ${on_string}: assembly graph with scaffolds" name="scaffold_graph">
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	207 <filter>scaffold_graph_out</filter>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	208 </data>
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	209 </outputs>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	210 <tests>
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	211 <test> <!-- Test 1 - basic test with k=33 -->
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	212 <param name="sc" value="false" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	213 <param name="careful" value="false" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	214 <param name="kmers" value="33" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	215 <param name="lib_type" value="paired_end" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	216 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	217 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	218 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
6 65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	219 <output name="out_contig_stats">
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	220 <assert_contents>
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	221 <has_text_matching expression="NODE_1\t1000"/>
6 65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	222 </assert_contents>
65c2d63fcbe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 iuc parents: 5 diff changeset	223 </output>
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	224 </test>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	225 <test> <!-- Test 2 - basic test with k=33 fasta input -->
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	226 <param name="sc" value="false" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	227 <param name="onlyassembler" value="true"/>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	228 <param name="careful" value="false" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	229 <param name="kmers" value="33" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	230 <param name="lib_type" value="paired_end" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	231 <param ftype="fasta" name="fwd_reads" value="ecoli_1K_1.fasta" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	232 <param ftype="fasta" name="rev_reads" value="ecoli_1K_2.fasta" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	233 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	234 <output name="out_contig_stats">
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	235 <assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	236 <has_text_matching expression="NODE_1\t1000"/>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	237 </assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	238 </output>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	239 </test>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	240 <test> <!-- Test 3 - basic test with k=33 and gzipped input -->
9 24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	241 <param name="sc" value="false" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	242 <param name="careful" value="false" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	243 <param name="kmers" value="33" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	244 <param name="lib_type" value="paired_end" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	245 <param ftype="fastq.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	246 <param ftype="fastq.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	247 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	248 <output name="out_contig_stats">
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	249 <assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	250 <has_text_matching expression="NODE_1\t1000"/>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	251 </assert_contents>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	252 </output>
24fffa4fee40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed iuc parents: 8 diff changeset	253 </test>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	254 <test> <!-- Test 4 - auto k -->
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	255 <param name="sc" value="false" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	256 <param name="careful" value="false" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	257 <param name="auto_kmer_choice" value="true" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	258 <param name="lib_type" value="paired_end" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	259 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	260 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	261 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	262 </test>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	263 <test> <!-- Test 5 - k=77 -->
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	264 <param name="sc" value="false" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	265 <param name="careful" value="false" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	266 <param name="kmers" value="77" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	267 <param name="lib_type" value="paired_end" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	268 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	269 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	270 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	271 </test>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	272 <test> <!-- Test 6 - test for extra graph outputs -->
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	273 <param name="sc" value="false" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	274 <param name="careful" value="false" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	275 <param name="kmers" value="33" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	276 <param name="lib_type" value="paired_end" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	277 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	278 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	279 <param name="contig_graph_out" value="true" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	280 <param name="scaffold_graph_out" value="true" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	281 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	282 <output name="out_contig_stats">
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	283 <assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	284 <has_text_matching expression="NODE_1\t1000"/>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	285 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	286 </output>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	287 <output name="contig_graph">
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	288 <assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	289 <has_text text=">EDGE_"/>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	290 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	291 </output>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	292 <output name="scaffold_graph">
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	293 <assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	294 <has_text text="NODE_"/>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	295 </assert_contents>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	296 </output>
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	297 </test>
10 b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	298 <test> <!-- Test 7 - basic test with k=33 and fastsanger input -->
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	299 <param name="sc" value="false" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	300 <param name="careful" value="false" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	301 <param name="kmers" value="33" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	302 <param name="lib_type" value="paired_end" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	303 <param ftype="fastqsanger" name="fwd_reads" value="ecoli_1K_1.fq" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	304 <param ftype="fastqsanger" name="rev_reads" value="ecoli_1K_2.fq" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	305 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	306 <output name="out_contig_stats">
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	307 <assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	308 <has_text_matching expression="NODE_1\t1000"/>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	309 </assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	310 </output>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	311 </test>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	312 <test> <!-- Test 8 - basic test with k=33 and fastsanger.gz input -->
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	313 <param name="sc" value="false" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	314 <param name="careful" value="false" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	315 <param name="kmers" value="33" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	316 <param name="lib_type" value="paired_end" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	317 <param ftype="fastqsanger.gz" name="fwd_reads" value="ecoli_1K_1.fq.gz" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	318 <param ftype="fastqsanger.gz" name="rev_reads" value="ecoli_1K_2.fq.gz" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	319 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	320 <output name="out_contig_stats">
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	321 <assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	322 <has_text_matching expression="NODE_1\t1000"/>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	323 </assert_contents>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	324 </output>
b8d633fbf5f5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 033c31f9e41c2869e195c66e5bf6cc2286062bd9 iuc parents: 9 diff changeset	325 </test>
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	326 </tests>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	327 <help>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	328 <![CDATA[
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	329 What it does
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	330
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	331 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.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	332
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	333 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 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	334
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	335 License
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	336
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	337 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	338
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	339 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.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	340
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	341 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.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	342
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	343 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	344
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	345 Acknowledgments
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	346
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	347 Original wrapper developed by Lionel Guy.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	348
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	349 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	350
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	351 Nicola Soranzo fixed various bugs.
7 9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	352
9006e5836729 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit cde78013f2df8cc06372d73f6332f7ab1f120a25 iuc parents: 6 diff changeset	353 Simon Gladman added fastg optional outputs.
5 909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	354 ]]>
909c315b656d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty iuc parents: 4 diff changeset	355 </help>
0 009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	356 <citations>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	357 <citation type="doi">10.1089/cmb.2012.0021</citation>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	358 </citations>
009c00203195 planemo upload commit 3fd243b12e91a3fe71083376f40e85647c8b892b-dirty nml parents: diff changeset	359 </tool>

Mercurial > repos > nml > spades

annotate spades.xml @ 13:b7829778729f draft